myrimatch: myrimatch.xml annotate

annotate myrimatch.xml @ 2:4bb0872e2b5f draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty

author	galaxyp
date	Thu, 02 Jun 2016 18:32:04 -0400
parents	cedaffdc5e40
children	c5e2f015165d

rev	line source
0 cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	1 <tool id="myrimatch" version="0.1.0" name="MyriMatch">
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>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	3 <requirements>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	4 <requirement type="package" version="3.0.8789">bumbershoot</requirement>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	5 </requirements>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	6 <stdio>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	7 <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	8 <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	9 source="both"
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	10 level="warning" />
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	11 </stdio>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	12 <command>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	13 <![CDATA[
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	14 #set $db_name = $ProteinDatabase.display_name.replace(".fasta", "") + ".fasta"
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	15 #if $OutputFormat.value == "mzid"
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	16 #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	17 #else
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	18 #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	19 #end if
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	20 #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	21 #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	22
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	23 #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	24 #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	25 #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	26 #end for
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	27 #for $mod in str($common_fixed_modifications).split(",")
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	28 #set $static_mods_str = $static_mods_str + " " + $mod.replace("_", " ")
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	29 #end for
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	30 #set $static_mods_str = $static_mods_str.strip()
0 cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	31
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 = ""
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	33 #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	34 #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	35 #end for
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	36 #for $mod in str($common_variable_modifications).split(",")
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	37 #set $dynamic_mods_str = $dynamic_mods_str + " " + $mod.replace("_", " ")
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	38 #end for
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	39 #set $dynamic_mods_str = $dynamic_mods_str.strip()
0 cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	40
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	41 ln -s '$input' '${input_name}' &&
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	42 ln -s '$ProteinDatabase' '${db_name}' &&
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	43 myrimatch -DecoyPrefix '${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	44 -ProteinDatabase '${db_name}'
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	45 -OutputFormat '${OutputFormat}'
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	46 '${input_name}'
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	47 -StaticMods '${static_mods_str}'
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	48 -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	49 -MaxDynamicMods $MaxDynamicMods
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	50 -CleavageRules '${CleavageRules}'
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	51 -MinTerminiCleavages $MinTerminiCleavages
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	52 -MaxMissedCleavages $MaxMissedCleavages
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	53 #set $precursor_type = $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	54 -PrecursorMzToleranceRule '${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	55 #if $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule == "auto" or $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule == "mono"
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	56 -MonoPrecursorMzTolerance '${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	57 #end if
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	58 #if $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule == "auto" or $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule == "avg"
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	59 -AvgPrecursorMzTolerance '${tolerance_options.precursor_tolerance.AvgPrecursorMzTolerance}${tolerance_options.precursor_tolerance.avg_precursor_mz_tolerance_units}'
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	60 #end if
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	61 -FragmentMzTolerance '${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	62 -UseSmartPlusThreeModel $advanced.UseSmartPlusThreeModel
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	63 -MinPeptideLength $advanced.MinPeptideLength
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	64 -MaxPeptideLength $advanced.MaxPeptideLength
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	65 -NumChargeStates $advanced.NumChargeStates
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	66 -MaxResultRank $advanced.MaxResultRank
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	67 #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	68 -MonoisotopeAdjustmentSet '$set'
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	69 #if $advanced.MaxPeakCount
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	70 -MaxPeakCount $advanced.MaxPeakCount
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	71 #end if
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	72 #if $advanced.fragmentation_rule.FragmentationAutoRule
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	73 -FragmentationAutoRule false -FragmentationRule 'manual:${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	74 #end if
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	75 &&
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	76 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	77 ]]>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	78 </command>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	79 <inputs>
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	80 <param name="input" type="data" format="mzml,mzxml,mgf,ms2,h5" 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	81 <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	82 <option value="pepXML">pepXML</option>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	83 <option value="mzid">mzIdentML</option>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	84 </param>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	85 <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	86 <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	87 <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	88 <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	89 <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	90 <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	91 <option value="TrypChymo">TrypChymo (combines "Trypsin/P" and "Chymotrypsin" cleavage rules)</option>
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	92 <option value="glutamyl endopeptidase">Glu-C</option>
0 cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	93 <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	94 <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	95 <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	96 <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	97 <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	98 <option value="Formic_acid">Formic acid</option>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	99 </param>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	100 <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	101 <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	102 <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	103 <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	104 </param>
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	105 <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." />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	106
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	107 <param name="common_fixed_modifications" type="select" label="Common Static Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	108 <option value="C_57.021464" selected="true">Carbamidomethyl C</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	109 <option value="(_144.102063">iTRAQ 4-plex N-term</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	110 <option value="K_144.102063">iTRAQ 4-plex K</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	111 <option value="(_225.155833">TMT 2-plex N-term</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	112 <option value="K_225.155833">TMT 2-plex K</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	113 <option value="(_229.162932">TMT 6-or-10-plex N-term</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	114 <option value="K_229.162932">TMT 6-or-10-plex K</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	115 <sanitizer invalid_char=""><valid initial="string.printable"><add value="("/><add value=")"/><add value=","/><add value="-"/><add value="_"/></valid><mapping initial="none"></mapping></sanitizer>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	116 </param>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	117 <param name="common_variable_modifications" type="select" label="Common Dynamic Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	118 <option value="K_*_42.010565">Acetylation K</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	119 <option value="(_*_42.010565">Acetylation Protein N-term</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	120 <option value="C_*_57.021464">Carbamidomethyl C</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	121 <option value="(_*_57.021464">Carbamidomethyl N-term</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	122 <option value="N_*_0.984016">Deamidation N</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	123 <option value="Q_*_0.984016">Deamidation Q</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	124 <option value="K_*_14.015650">Methylation K</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	125 <option value="M_*_15.994915" selected="true">Oxidation M</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	126 <option value="S_*_97.976896">Phosphorylation S</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	127 <option value="T_*_97.976896">Phosphorylation T</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	128 <option value="Y_*_97.976896">Phosphorylation Y</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	129 <option value="(E_*_-18.010565">Pyro-glu from E</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	130 <option value="(Q_*_-17.026549">Pyro-glu from Q</option>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	131 <sanitizer invalid_char=""><valid initial="string.printable"><add value="("/><add value=")"/><add value=","/><add value="_"/><add value="*"/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	132 </param>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	133
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	134 <repeat name="StaticMods" title="Custom 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	135 <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	136 <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	137 </param>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	138 <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	139 </repeat>
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	140 <repeat name="DynamicMods" title="Custom 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	141 <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	142 <sanitizer>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	143 <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	144 <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	145 <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	146 <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	147 <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	148 <add value="."/>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	149 <add value="!"/>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	150 </valid>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	151 </sanitizer>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	152 </param>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	153 <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	154 </repeat>
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	155
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	156 <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	157 <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	158 <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	159 <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	160 <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	161 <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	162 <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	163 </param>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	164 <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	165 <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	166 <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	167 <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	168 <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	169 </param>
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	170 <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	171 <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	172 <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	173 <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	174 </param>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	175 </when>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	176 <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	177 <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	178 <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	179 <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	180 <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	181 </param>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	182 </when>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	183 <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	184 <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	185 <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	186 <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	187 <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	188 </param>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	189 </when>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	190 </conditional>
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	191 <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	192 <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	193 <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	194 <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	195 </param>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	196 </section>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	197 <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	198 <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	199 <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	200 <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	201 <when value="false" />
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	202 <when value="true">
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	203 <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	204 </when>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	205 </conditional>
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	206 <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	207 <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	208 <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	209 <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	210 <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	211 <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	212 <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	213 </param>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	214 </section>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	215 </inputs>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	216 <outputs>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	217 <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	218 <change_format>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	219 <when input="OutputFormat" value="mzid" format="mzid" />
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	220 </change_format>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	221 </data>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	222 </outputs>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	223 <tests>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	224 <test>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	225 <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	226 <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	227 <param name="DecoyPrefix" value="XXX_" />
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	228 <param name="common_fixed_modifications" value="" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	229 <param name="common_variable_modifications" value="" />
0 cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	230 <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	231 <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	232 <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	233 <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	234 <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	235 <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	236 <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	237 <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	238 <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	239 <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	240 <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	241 <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	242 <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	243 <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	244 <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	245 <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	246 <param name="UseSmartPlusThreeModel" value="false" />
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	247 <output name="output" file="201208-378803-mm.pepXML" lines_diff="12" />
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	248 </test>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	249 <test>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	250 <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	251 <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	252 <param name="DecoyPrefix" value="XXX_" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	253 <param name="StaticMods_0\|aa" value="C" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	254 <param name="StaticMods_0\|mass" value="58.00548" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	255 <param name="DynamicMods_0\|motif" value="M" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	256 <param name="DynamicMods_0\|mass" value="15.9949" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	257 <param name="DynamicMods_1\|motif" value="(Q" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	258 <param name="DynamicMods_1\|mass" value="-17.026" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	259 <param name="common_fixed_modifications" value="" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	260 <param name="common_variable_modifications" value="Q__0.984016,N__0.984016" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	261 <param name="PrecursorMzToleranceRule" value="mono" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	262 <param name="MonoPrecursorMzTolerance" value="50" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	263 <param name="MinTerminiCleavages" value="1" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	264 <param name="MaxMissedCleavages" value="2" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	265 <param name="MaxDynamicMods" value="2" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	266 <param name="NumChargeStates" value="5" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	267 <param name="MaxResultRank" value="3" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	268 <param name="MonoisotopeAdjustmentSet" value="[-1,2]" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	269 <param name="UseSmartPlusThreeModel" value="false" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	270 <output name="output" file="201208-378803-mm.pepXML" lines_diff="14" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	271 </test>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	272 <test>
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	273 <param name="input" value="input/201208-378803.mzML" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	274 <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
0 cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	275 <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	276 <param name="DecoyPrefix" value="XXX_" />
2 4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	277 <param name="common_fixed_modifications" value="" />
4bb0872e2b5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty galaxyp parents: 0 diff changeset	278 <param name="common_variable_modifications" value="" />
0 cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	279 <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	280 <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	281 <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	282 <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	283 <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	284 <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	285 <param name="MonoisotopeAdjustmentSet" value="0" />
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	286 <output name="output" file="201208-378803-mm-15ppm-fully-tryptic.pepXML" lines_diff="12" />
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	287 </test>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	288 </tests>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	289 <help>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	290 <![CDATA[
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	291 What it does
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	292
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	293 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	294 ]]>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	295 </help>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	296 <citations>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	297 <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	298 <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	299 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	300 </citations>
cedaffdc5e40 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty galaxyp parents: diff changeset	301 </tool>

Mercurial > repos > galaxyp > myrimatch

annotate myrimatch.xml @ 2:4bb0872e2b5f draft