metfrag: metfrag.xml annotate

annotate metfrag.xml @ 7:0b3816a7a14b draft

planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6dc5d494a84dd572f277dcd1c979e6edfb40383d

author	tomnl
date	Thu, 05 Sep 2019 06:48:28 -0400
parents	ceb9bd68f6bc
children	9a3019c609d9

rev	line source
7 0b3816a7a14b planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6dc5d494a84dd572f277dcd1c979e6edfb40383d tomnl parents: 6 diff changeset	1 <tool id="metfrag" name="MetFrag" version="2.4.5+galaxy0.1.12">
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	2 <description> </description>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	3 <requirements>
5 c53ed894d736 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 826659b9105b635cf240474428122f5a269f5c88 tomnl parents: 4 diff changeset	4 <requirement type="package" version="2.4.5">metfrag</requirement>
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	5 </requirements>
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	6 <stdio>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	7 <regex match="Cannot allocate memory"
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	8 source="stderr"
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	9 level="fatal_oom"
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	10 description="Out of memory error occurred" />
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	11 </stdio>
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	12 <command detect_errors="exit_code">
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	13 <![CDATA[
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	14
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	15 python $__tool_directory__/metfrag.py
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	16 --input_pth "$input"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	17 --result_pth '$results'
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	18 --temp_dir './temp/'
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	19
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	20 --cores_top_level \${GALAXY_SLOTS:-4}
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	21
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	22 --MetFragDatabaseType '$db_select.MetFragDatabaseType'
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	23
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	24 #if $db_select.MetFragDatabaseType == "LocalCSV":
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	25 --LocalDatabasePath '$db_select.LocalDatabasePath'
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	26 #elif $db_select.MetFragDatabaseType == "MetChem":
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	27 --LocalMetChemDatabaseServerIp '$db_select.LocalMetChemDatabaseServerIp'
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	28 #end if
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	29
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	30 --DatabaseSearchRelativeMassDeviation $DatabaseSearchRelativeMassDeviation
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	31 --FragmentPeakMatchRelativeMassDeviation $FragmentPeakMatchRelativeMassDeviation
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	32 --FragmentPeakMatchAbsoluteMassDeviation $FragmentPeakMatchAbsoluteMassDeviation
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	33 --polarity '$polarity'
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	34
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	35 --MetFragScoreTypes '$suspectlist.MetFragScoreTypes'
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	36 --MetFragScoreWeights '$suspectlist.MetFragScoreWeights'
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	37
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	38 #if $suspectlist.suspectselector == 'includesuspects':
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	39 #if $suspectlist.includesuspects_default_cond:
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	40 --ScoreSuspectLists '$__tool_directory__/test-data/UNPD_DB.inchikeys.txt'
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	41 #else
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	42 --ScoreSuspectLists '$suspectlist.includesuspects_custom_cond.ScoreSuspectLists'
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	43 #end if
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	44 #end if
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	45
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	46 --meta_select_col $meta_select_col
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	47 --minMSMSpeaks $minMSMSpeaks
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	48 --schema $schema
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	49
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	50 $PreProcessFilter.UnconnectedCompoundFilter
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	51 $PreProcessFilter.IsotopeFilter
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	52
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	53
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	54 --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements'
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	55 --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements'
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	56 --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList'
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	57 --FilterSmartsExclusionList '$PreProcessFilter.FilterSmartsExclusionList'
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	58 --FilterIncludedElements '$PreProcessFilter.FilterIncludedElements'
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	59 --FilterExcludedElements '$PreProcessFilter.FilterExcludedElements'
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	60 --FilterIncludedExclusiveElements '$PreProcessFilter.FilterIncludedExclusiveElements'
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	61
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	62 $skip_invalid_adducts
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	63 --score_thrshld $PostProcessFilter.score_thrshld
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	64 --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	65
7 0b3816a7a14b planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6dc5d494a84dd572f277dcd1c979e6edfb40383d tomnl parents: 6 diff changeset	66
0b3816a7a14b planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6dc5d494a84dd572f277dcd1c979e6edfb40383d tomnl parents: 6 diff changeset	67
0b3816a7a14b planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6dc5d494a84dd572f277dcd1c979e6edfb40383d tomnl parents: 6 diff changeset	68
0b3816a7a14b planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6dc5d494a84dd572f277dcd1c979e6edfb40383d tomnl parents: 6 diff changeset	69
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	70 ]]></command>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	71 <inputs>
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	72
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	73 <param name="input" type="data" format="msp,txt" label="MSP file (Output from Create MSP tool)"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	74 <conditional name="db_select">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	75 <param name="MetFragDatabaseType" type="select" label="Choose Compound Database"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	76 argument="--MetFragDatabaseType">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	77 <option value="PubChem" selected="true">PubChem</option>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	78 <option value="KEGG">KEGG</option>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	79 <option value="LocalCSV">Local database (csv)</option>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	80 <option value="MetChem">MetChem</option>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	81 </param>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	82 <when value="MetChem">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	83 <param name="LocalMetChemDatabaseServerIp" type="text" label="MetChem URL"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	84 argument="--LocalMetChemDatabaseServerIp" />
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	85 </when>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	86 <when value="LocalCSV">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	87 <param name="LocalDatabasePath" type="data" format="csv" label="Local database of compounds (CSV format)" argument="--LocalDatabasePath"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	88 </when>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	89 <when value="KEGG">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	90 </when>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	91 <when value="PubChem">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	92 </when>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	93 </conditional>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	94 <param name="DatabaseSearchRelativeMassDeviation" type="float" value="10"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	95 label="Relative Mass Deviation for database search (ppm)" argument="--DatabaseSearchRelativeMassDeviation"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	96 help="A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	97 <param name="FragmentPeakMatchRelativeMassDeviation" type="float" value="5"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	98 label="Fragment Peak Match Relative Mass Deviation (ppm)" argument="--FragmentPeakMatchRelativeMassDeviation"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	99 help="Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks" />
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	100 <param name="FragmentPeakMatchAbsoluteMassDeviation" type="float" value="0.001"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	101 label="Fragment Peak Match Absolute Mass Deviation (Da)" argument="FragmentPeakMatchAbsoluteMassDeviation"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	102 help="Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks" />
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	103 <param name="polarity" type="select" label="Polarity" help="The polarity used for the mode of acquisition">
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	104 <option value="pos" selected="true">Positive</option>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	105 <option value="neg">Negative</option>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	106 </param>
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	107 <param name="schema" type="select" label="Schema"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	108 help="The schema used for the MSP file (auto will try automatically determine the schema)">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	109 <option value="auto" selected="True">Auto</option>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	110 <option value="msp" >Generic MSP</option>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	111 <option value="massbank">MassBank</option>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	112 </param>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	113 <param name="meta_select_col" type="select" label="Choose how additional metadata columns are extracted"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	114 help="The MetFrag output can have additional meta data columns added, these can be either extracted
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	115 from all MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	116 can be added from the 'Name' or 'RECORD_TITLE' parameter by splitting on \| and :
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	117 e.g. 'MZ:100.2 \| RT:20 \| xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	118 <option value="name" selected="true">Extra metadata columns from the Name or RECORD_TITLE</option>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	119 <option value="name_split" >Extra metadata columns from the Name or RECORD_TITLE (each column is split on "\|" and ":" ) </option>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	120 <option value="all">Extra metadata columns from all MSP parameters</option>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	121 </param>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	122
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	123 <conditional name="suspectlist">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	124 <param name="suspectselector" type="select" optional="False" label="Suspect list" help="Choose whether to include a suspect list">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	125 <option value="includesuspects" >Include suspect list</option>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	126 <option value="excludesuspects" selected="True">Do not include suspect list</option>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	127 </param>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	128 <when value="includesuspects">
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	129 <conditional name="includesuspects_default_cond">
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	130 <param name="includesuspects_default_bool" type="boolean" label="Use default list of suspect compounds?"
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	131 help="Either provide a file containing a list of suspect compounds or a default file
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	132 of of an aggregated list of in silico predicted MS/MS spectra of natural products
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	133 from the Universal Natural Products Database (http://pkuxxj.pku.edu.cn/UNPD/index.php).
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	134 The list is an aggregated version of the github repository https://github.com/oolonek/ISDB/tree/master/Data/dbs."/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	135 <when value="true">
5 c53ed894d736 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 826659b9105b635cf240474428122f5a269f5c88 tomnl parents: 4 diff changeset	136 </when>
c53ed894d736 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 826659b9105b635cf240474428122f5a269f5c88 tomnl parents: 4 diff changeset	137 <when value="false">
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	138 <param name="ScoreSuspectLists" type="data" format="txt" optional="False" label="Suspect list file"
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	139 help="File containing a list of suspects inchikeys" />
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	140 </when>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	141 </conditional>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	142
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	143 <param name="MetFragScoreTypes" type="text" value="FragmenterScore,OfflineMetFusionScore,SuspectListScore" optional="False" label="MetFrag Score Types" help="The type of scores MetFrag is calculating. Please do not change the value unless you know what you are doing." />
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	144 <param name="MetFragScoreWeights" type="text" value="0.4,0.6,1.0" optional="False" label="MetFrag Score Weights" help="The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100 percent." />
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	145 </when>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	146 <when value="excludesuspects">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	147 <param name="MetFragScoreTypes" type="text" value="FragmenterScore,OfflineMetFusionScore" optional="False" label="MetFrag Score Types" help="The type of scores MetFrag is calculating. Please do not change the value unless you know what you are doing." />
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	148 <param name="MetFragScoreWeights" type="text" value="1.0,1.0" optional="False" label="MetFrag Score Weights" help="The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100 percent." />
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	149 </when>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	150 </conditional>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	151
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	152 <param name="minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/>
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	153 <param name="skip_invalid_adducts" type="boolean" label="Skip invalid or undefined adduct types?"
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	154 truevalue="--skip_invalid_adducts" falsevalue=""
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	155 help="If no adduct type is provided within the MSP file or if the adduct type is not usable
5 c53ed894d736 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 826659b9105b635cf240474428122f5a269f5c88 tomnl parents: 4 diff changeset	156 with MetFrag, set to 'yes' if these spectra should be skipped or 'no' if the default
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	157 of [M+H]+ for pos data or [M-H]- for neg data should be used"/>
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	158 <section name="PreProcessFilter" title="PreProcessing filters" expanded="False">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	159 <param name="UnconnectedCompoundFilter" type="boolean" checked="false" truevalue="--UnconnectedCompoundFilter"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	160 falsevalue="" label="filter non-connected compounds (e.g. salts)" help=""/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	161 <param name="IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter" falsevalue=""
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	162 label="filter compounds containing non-standard isotopes" help=""/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	163 <param name="FilterMinimumElements" type="text" label="Minimum Elements Filter"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	164 help="Filter by minimum of contained elements. Ex: N2O3 include compounds with at least 2 nitrogens and 3 oxygens"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	165 <param name="FilterMaximumElements" type="text" label="Maximum Elements Filter"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	166 help="Filter by maximum of contained elements. Ex: N5O7 filter out compounds with at maximum 5 nitrogens and 7 oxygens"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	167 <param name="FilterSmartsInclusionList" type="text" label="Include substructures"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	168 help="Filter by presence of defined sub-structures. Ex: c1ccccc1 include compounds containing benzene"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	169 <param name="FilterSmartsExclusionList" type="text" label="Exclude substructures"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	170 help="Filter by absence of defined sub-structures. Ex: [OX2H] filter out compounds containing hydroxyl groups"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	171 <param name="FilterIncludedElements" type="text" label="Include elements"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	172 help="Filter by presence of defined elements (other elements are allowed). Ex: 'N,O' include compounds containing nitrogen and oxygen" />
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	173 <param name="FilterIncludedExclusiveElements" type="text" label="Include elements (exclusive)"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	174 help="Filter by presence of defined elements (no other elements are allowed). Ex: 'N,O' include compounds only composed of nitrogen and oxygen" />
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	175 <param name="FilterExcludedElements" type="text" label="Exclude elements"
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	176 help="Filter by absence of defined sub-structures. Ex: 'Cl,Br' filter out compounds including bromine or chlorine"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	177 </section>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	178
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	179 <section name="PostProcessFilter" title="PostProcessing filters" expanded="False">
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	180 <param name="score_thrshld" type="float" label="Threshold for score after MetFrag search" max="1" min="0" value="0"/>
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	181 <param name="pctexplpeak_thrshld" type="float" label="Minimum percentage of explain peaks" max="100" min="0" value="0"/>
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	182 </section>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	183
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	184 </inputs>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	185 <outputs>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	186 <data name="results" format="tabular" label="${tool.name} results of ${input.name}" />
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	187 </outputs>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	188 <tests>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	189 <test>
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	190 <!-- Test "massbank" style data format -->
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	191 <param name="input" value="massbank_format.txt"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	192 <param name="schema" value="massbank"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	193 <param name="MetFragDatabaseType" value="LocalCSV"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	194 <param name="LocalDatabasePath" value="demo_db.csv"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	195 <output name="results" file="metfrag_massbank.tabular"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	196 </test>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	197 <test>
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	198 <!-- Test "generic" style data format -->
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	199 <param name="input" value="generic_format.msp"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	200 <param name="schema" value="msp"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	201 <param name="MetFragDatabaseType" value="LocalCSV"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	202 <param name="LocalDatabasePath" value="demo_db.csv"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	203 <output name="results" file="metfrag_msp.tabular"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	204 </test>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	205 <test>
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	206 <!-- Test PubChem API with "winter" dataset -->
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	207 <param name="input" value="winter_pos.msp"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	208 <param name="PostProcessFilter\|score_thrshld" value="0.9"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	209 <param name="MetFragDatabaseType" value="PubChem"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	210 <output name="results" file="winter_pos.tabular"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	211 </test>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	212 <test>
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	213 <!-- Test actual MassBank data for Glucose -->
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	214 <param name="input" value="RP022611.txt"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	215 <param name="MetFragDatabaseType" value="LocalCSV"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	216 <param name="LocalDatabasePath" value="demo_db.csv"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	217 <output name="results" file="RP022611.tabular"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	218 </test>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	219 <test>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	220 <!-- Test actual MassBank data for Glucose (all metadata columns in output-->
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	221 <param name="input" value="RP022611.txt"/>
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	222 <param name="schema" value="massbank"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	223 <param name="MetFragDatabaseType" value="LocalCSV"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	224 <param name="LocalDatabasePath" value="demo_db.csv"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	225 <param name="meta_select_col" value="all"/>
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	226 <output name="results" file="RP022611_all_col.tabular"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	227 </test>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	228 <test>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	229 <!-- Test actual MassBank data for Glucose (include suspect list - default)-->
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	230 <param name="input" value="RP022611.txt"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	231 <param name="schema" value="massbank"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	232 <param name="suspectlist\|suspectselector" value="includesuspects"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	233 <param name="suspectlist\|includesuspects_default_cond\|includesuspects_default_bool" value="true"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	234 <param name="suspectlist\|MetFragScoreTypes" value="FragmenterScore,OfflineMetFusionScore,SuspectListScore"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	235 <param name="suspectlist\|MetFragScoreWeights" value="0.4,0.6,1.0"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	236 <output name="results" file="RP022611_suspect_default.txt"/>
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	237 </test>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	238 <test>
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	239 <!-- Test actual MassBank data for Glucose (include suspect list - custom)-->
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	240 <param name="input" value="RP022611.txt"/>
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	241 <param name="schema" value="massbank"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	242 <param name="suspectlist\|suspectselector" value="includesuspects"/>
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	243 <param name="suspectlist\|includesuspects_default_cond\|includesuspects_default_bool" value="false"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	244 <param name="suspectlist\|includesuspects_default_cond\|ScoreSuspectLists" value="UNPD_DB.inchikeys.txt"/>
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	245 <param name="suspectlist\|MetFragScoreTypes" value="FragmenterScore,OfflineMetFusionScore,SuspectListScore"/>
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	246 <param name="suspectlist\|MetFragScoreWeights" value="0.4,0.6,1.0"/>
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	247 <output name="results" file="RP022611_suspect_default.txt"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	248 </test>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	249 <test>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	250 <!-- Test actual MassBank data for Glucose (include suspect list - custom)-->
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	251 <param name="input" value="invalid_adduct.msp"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	252 <param name="skip_invalid_adducts" value="true"/>
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	253 <output name="results" file="invalid_adduct_result.txt"/>
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	254 </test>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	255 </tests>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	256 <help>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	257 -------
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	258 MetFrag
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	259 -------
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	260
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	261 Description
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	262 -----------
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	263
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	264 MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment.
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	265
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	266 Website: http://c-ruttkies.github.io/MetFrag
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	267
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	268 Parameters
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	269 ----------
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	270
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	271 \1. MSP file
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	272
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	273 MSP file created using Create MSP tool
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	274
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	275 \2a. MetFragDatabaseType (public databases)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	276
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	277 * PubChem
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	278
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	279 * KEGG
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	280
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	281
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	282 \2b. MetFragDatabaseType (local CSV file database)
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	283
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	284 Custom database file in CSV format with the following structure:
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	285
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	286 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	287 \| Identifier \| MonoisotopicMass \| SMILES \| InChI \| Name \|...\|
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	288 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	289 \| HMDB0000123 \| 75.03202841 \| NCC(O)=O \| InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) \| Glycine \|...\|
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	290 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	291 \| HMDB0002151 \| 78.0139355 \| CS(C)=O \| InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 \| Dimethyl sulfoxide \|...\|
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	292 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	293 \| ... \| ... \| ... \| ... \| ... \|...\|
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	294 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	295
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	296
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	297 Table continued:
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	298
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	299 +---+------------------+-----------------------------+------------------+------------+-------------+
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	300 \|...\| MolecularFormula \| InChIKey \| InChIKey1 \| InChIKey2 \| InChIKey3 \|
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	301 +---+------------------+-----------------------------+------------------+------------+-------------+
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	302 \|...\| C2H5NO2 \| DHMQDGOQFOQNFH-UHFFFAOYSA-N \| DHMQDGOQFOQNFH \| UHFFFAOYSA \| N \|
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	303 +---+------------------+-----------------------------+------------------+------------+-------------+
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	304 \|...\| C2H6OS \| IAZDPXIOMUYVGZ-UHFFFAOYSA-N \| IAZDPXIOMUYVGZ \| UHFFFAOYSA \| N \|
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	305 +---+------------------+-----------------------------+------------------+------------+-------------+
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	306 \|...\| ... \| ... \| ... \| ... \| ... \|
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	307 +---+------------------+-----------------------------+------------------+------------+-------------+
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	308
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	309
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	310 \2b. MetFragDatabaseType MetChem local database
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	311
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	312 MetChem is a modified PubChem database and can be used in replace of PubChem
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	313 for performing API calls to the public PubChem instance. Details regarding how to serve the database can be located
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	314 here:
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	315
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	316 \3. Database Search Relative Mass Deviation - ppm
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	317
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	318 A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses.
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	319
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	320 \4. Fragment Peak Match Relative Mass Deviation - ppm
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	321
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	322 Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks.
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	323
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	324 \5. Fragment Peak Match Absolute Mass Deviation (Da)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	325
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	326 Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks.
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	327
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	328 \6. Polarity
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	329
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	330 The polarity used for the mode of acquisition.
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	331
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	332 \7. Schema
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	333
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	334 The Schema used by the MSP file (e.g. generic MSP format or MassBank format)
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	335
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	336 \8. Suspect list
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	337
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	338 Choose whether to include a file containing a list of suspects.
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	339
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	340 \9. MetFrag Score Types
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	341
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	342 The type of scores MetFrac is using for the calculations. Please do not change the values unless you know what you are doing!
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	343
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	344 \10. MetFrag Score Weights
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	345
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	346 The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100%.
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	347
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	348 \11. MetFrag Database Type
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	349
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	350 Database to choose from.
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	351
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	352 \12. minMSMSpeaks
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	353
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	354 Minimum MS/MS peaks within a MS/MS spectra to be used for the MetFrag calculation
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	355
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	356 \13. PreProcessFilter
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	357
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	358 Various filters can be performed on the potential compounds prior to predicting the in silico spectra
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	359
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	360 \14. PostProcessFilter
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	361
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	362 To make the output more manageble results below certain criteria can be removed from the various filters can be
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	363 performed on the potential compounds prior to predicting the in silico spectra
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	364
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	365 Additional notes
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	366 --------------------
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	367
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	368 The following adducts (and format) are currently supported in the MSP file. The neutral mass is automatically
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	369 calculated for the precursor m/z by subtracting the adduct mass
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	370
4 eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	371 - '[M+H]+': 1.007276,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	372 - '[M+NH4]+': 18.034374,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	373 - '[M+Na]+': 22.989218,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	374 - '[M+K]+': 38.963158,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	375 - '[M+CH3OH+H]+': 33.033489,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	376 - '[M+ACN+H]+': 42.033823,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	377 - '[M+ACN+Na]+': 64.015765,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	378 - '[M+2ACN+H]+': 83.06037,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	379 - '[M-H]-': -1.007276,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	380 - '[M+Cl]-': 34.969402,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	381 - '[M+HCOO]-': 44.99819,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	382 - '[M-H+HCOOH]-': 44.99819,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	383 - '[M+CH3COO]-': 59.01385,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4 tomnl parents: 3 diff changeset	384 - '[M-H+CH3COOH]-': 59.01385
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	385
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	386 Developers and contributors
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	387 ---------------------------
1 c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	388 - Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	389 - Julien Saint-Vanne (julien.saint-vanne@sb-roscoff.fr) - ABiMS (France)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	390 - Tom Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	391 - Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	392 - Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	393 - Payam Emami (payam.emami@medsci.uu.se) - Uppsala Universitet (Sweden)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty tomnl parents: 0 diff changeset	394 - Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)
0 75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	395
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	396
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	397 </help>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	398 <citations>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	399 <citation type="doi">10.1186/s13321-016-0115-9</citation>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	400 </citations>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14 tomnl parents: diff changeset	401 </tool>

Mercurial > repos > tomnl > metfrag

annotate metfrag.xml @ 7:0b3816a7a14b draft