tracegroomer: tracegroomer.xml annotate

annotate tracegroomer.xml @ 1:c6a7bbc6066d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2

author	iuc
date	Tue, 03 Sep 2024 19:22:57 +0000
parents	5f7d672647b0
children

rev	line source
0 5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	1 <tool id="tracegroomer" name="tracegroomer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	2 <description>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	3 TraceGroomer is a solution to format and normalize files for DIMet tool
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	4 </description>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	5 <macros>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	6 <import>macros.xml</import>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	7 </macros>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	8 <expand macro="requirements"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	9 <command detect_errors="exit_code"><![CDATA[
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	10 mkdir -p config &&
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	11 #if $sample_metadata_path:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	12 ln -s '$sample_metadata_path' ./sample_metadata.csv &&
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	13 #end if
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	14 #if $type_of_file.type_of_file_selector == "rule_tsv":
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	15 #if $variable_metadata_path:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	16 ln -s '$variable_metadata_path' ./variableMetadata.tsv &&
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	17 #end if
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	18 #end if
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	19 ln -s '$param_file' config/config.yaml &&
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	20 python3 -m tracegroomer
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	21 -cf 'config/config.yaml'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	22 -lm '${labeled_metabo_file}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	23 -tf '${type_of_file_selector}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	24 --isosprop_min_admitted ${isosprop_min_admitted}
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	25 #if $amount_material:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	26 --amountMaterial_path '${amount_material}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	27 #end if
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	28 #if $remove_these_metabolites:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	29 --remove_these_metabolites '${remove_these_metabolites}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	30 #end if
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	31 #if $advanced_options.use_internal_standard:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	32 --use_internal_standard ${use_internal_standard}
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	33 #end if
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	34 $alternative_div_amount_material
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	35 $div_isotopologues_by_amount_material
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	36 $isotopologues_preview
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	37 $fractions_stomp_values
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	38 $subtract_blankavg
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	39 $under_detection_limit_set_nan
1 c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	40 -ox $output_files_extension &&
0 5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	41 #if $type_of_file.type_of_file_selector == "IsoCor_out_tsv":
1 c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	42 cp -rf '${AbundanceCorrected}.${output_files_extension}' '${AbundanceCorrected}' &&
c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	43 cp -rf '${MeanEnrichment13C}.${output_files_extension}' '${MeanEnrichment13C}' &&
c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	44 cp -rf '${IsotopologuesProp}.${output_files_extension}' '${IsotopologuesProp}' &&
c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	45 cp -rf '${IsotopologuesAbs}.${output_files_extension}' '${IsotopologuesAbs}'
0 5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	46 #else if $type_of_file.type_of_file_selector == "rule_tsv":
1 c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	47 cp -rf '${Absolute_isotopologue_abundances}.${output_files_extension}' '${Absolute_isotopologue_abundances}'
0 5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	48 #else if $type_of_file.type_of_file_selector == "generic_xlsx":
1 c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	49 cp -rf '${sheetname}.${output_files_extension}' '${isotopologuesCorrValues}'
0 5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	50 #else:
1 c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	51 cp -rf '${raw_abundance_sheet_name}.${output_files_extension}' '${rawAbundances}' &&
c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	52 cp -rf '${frac_contribution_sheet_name}.${output_files_extension}' '${FracContribution_C}' &&
c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	53 cp -rf '${corrected_isotopologues_sheet_name}.${output_files_extension}' '${CorrectedIsotopologues}'
0 5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	54 #end if
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	55
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	56 ]]></command>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	57
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	58 <configfiles>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	59 <configfile name="param_file"><![CDATA[
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	60 groom_out_path: '.'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	61 metadata: sample_metadata
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	62 #if $type_of_file.type_of_file_selector == "IsoCor_out_tsv":
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	63 abundances: '${AbundanceCorrected}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	64 mean_enrichment: '${MeanEnrichment13C}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	65 isotopologue_proportions: '${IsotopologuesProp}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	66 isotopologues: '${IsotopologuesAbs}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	67 #end if
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	68
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	69 #if $type_of_file.type_of_file_selector == "VIBMEC_xlsx":
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	70 abundances: '${raw_abundance_sheet_name}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	71 mean_enrichment: '${frac_contribution_sheet_name}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	72 isotopologue_proportions: '${corrected_isotopologues_sheet_name}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	73 isotopologues: null
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	74 #end if
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	75
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	76 #if $type_of_file.type_of_file_selector == "generic_xlsx":
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	77 abundances: null
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	78 mean_enrichment: null
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	79 isotopologue_proportions: null
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	80 isotopologues: '${sheetname}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	81 #end if
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	82
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	83 #if $type_of_file.type_of_file_selector == "rule_tsv":
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	84 abundances: null
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	85 mean_enrichment: null
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	86 isotopologue_proportions: null
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	87 isotopologues: '${Absolute_isotopologue_abundances}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	88 variable_description : variableMetadata
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	89 columns_variable_description:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	90 identifier: '${columns_variable_metadata_description.identifier}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	91 compound: '${columns_variable_metadata_description.compound}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	92 isotopologue_number : '${columns_variable_metadata_description.isotopologue_number}'
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	93 #end if
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	94 ]]></configfile>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	95 </configfiles>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	96 <inputs>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	97 <expand macro="input_datasets"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	98 <expand macro="advanced_options"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	99 </inputs>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	100 <outputs>
1 c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	101 <data label="Total metabolite abundances" name="AbundanceCorrected" format="tabular">
0 5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	102 <filter>type_of_file['type_of_file_selector'] == 'IsoCor_out_tsv'</filter>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	103 </data>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	104 <data label="Mean enrichment data" name="MeanEnrichment13C" format="tabular">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	105 <filter>type_of_file['type_of_file_selector'] == 'IsoCor_out_tsv'</filter>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	106 </data>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	107 <data label="Isotopologue proportional abundances" name="IsotopologuesProp" format="tabular">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	108 <filter>type_of_file['type_of_file_selector'] == 'IsoCor_out_tsv'</filter>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	109 </data>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	110 <data label="Absolute isotopologue abundances" name="IsotopologuesAbs" format="tabular">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	111 <filter>type_of_file['type_of_file_selector'] == 'IsoCor_out_tsv'</filter>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	112 </data>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	113 <data label="Absolute isotopologue abundances for rule tsv" name="Absolute_isotopologue_abundances" format="tabular">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	114 <filter>type_of_file['type_of_file_selector'] == 'rule_tsv'</filter>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	115 </data>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	116 <data label="Absolute isotopologue abundances for generic xlsx" name="isotopologuesCorrValues" format="tabular">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	117 <filter>type_of_file['type_of_file_selector'] == 'generic_xlsx'</filter>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	118 </data>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	119 <data label="raw abundances for VIBMEC" name="rawAbundances" format="tabular">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	120 <filter>type_of_file['type_of_file_selector'] == 'VIBMEC_xlsx'</filter>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	121 </data>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	122 <data label="Mean enrichment data for VIBMEC" name="FracContribution_C" format="tabular">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	123 <filter>type_of_file['type_of_file_selector'] == 'VIBMEC_xlsx'</filter>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	124 </data>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	125 <data label="Isotopologue corrected abundances for VIBMEC" name="CorrectedIsotopologues" format="tabular">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	126 <filter>type_of_file['type_of_file_selector'] == 'VIBMEC_xlsx'</filter>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	127 </data>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	128 </outputs>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	129 <tests>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	130 <test expect_num_outputs="4">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	131 <param name="labeled_metabo_file" ftype="tabular" value="TRACER_IsoCor_out_example.tsv"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	132 <param name="sample_metadata_path" ftype="tabular" value="sampleMetadata_1.csv"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	133 <param name="type_of_file_selector" value="IsoCor_out_tsv"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	134 <section name="advanced_options">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	135 <param name="isosprop_min_admitted" ftype="float" value='-0.5'/>
1 c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	136 <param name="alternative_div_amount_material" ftype="boolean" value='true'/>
c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	137 <param name="div_isotopologues_by_amount_material" ftype="boolean" value='true'/>
c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	138 <param name="isotopologues_preview" ftype="boolean" value='false'/>
c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	139 <param name="fractions_stomp_values" ftype="boolean" value='true'/>
c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	140 <param name="subtract_blankavg" ftype="boolean" value='true'/>
0 5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	141 <param name="under_detection_limit_set_nan" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	142 </section>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	143 <output file="AbundanceCorrected.tsv" name="AbundanceCorrected" ftype="tabular"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	144 <output file="IsotopologuesAbs.tsv" name="IsotopologuesAbs" ftype="tabular"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	145 <output file="IsotopologuesProp.tsv" name="IsotopologuesProp" ftype="tabular"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	146 <output file="MeanEnrichment13C.tsv" name="MeanEnrichment13C" ftype="tabular"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	147 </test>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	148 <test expect_num_outputs="1">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	149 <param name="labeled_metabo_file" ftype="tabular" value="TRACER_dataMatrix.tsv"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	150 <param name="sample_metadata_path" ftype="tabular" value="sampleMetadata_2.tsv"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	151 <param name="variable_metadata_path" ftype="tabular" value="variableMetadata.tsv"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	152 <param name="type_of_file_selector" value="rule_tsv"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	153 <section name="advanced_options">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	154 <param name="isosprop_min_admitted" ftype="float" value='-0.5'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	155 <param name="alternative_div_amount_material" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	156 <param name="div_isotopologues_by_amount_material" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	157 <param name="isotopologues_preview" ftype="boolean" value='false'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	158 <param name="fractions_stomp_values" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	159 <param name="subtract_blankavg" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	160 <param name="under_detection_limit_set_nan" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	161 </section>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	162 <output file="Absolute_isotopologue_abundances.tsv" name="Absolute_isotopologue_abundances" ftype="tabular"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	163 </test>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	164 <test expect_num_outputs="1">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	165 <param name="labeled_metabo_file" ftype="xlsx" value="TRACER_generic_sheet.xlsx"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	166 <param name="sample_metadata_path" ftype="tabular" value="sampleMetadata_3.csv"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	167 <param name="type_of_file_selector" value="generic_xlsx"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	168 <section name="advanced_options">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	169 <param name="isosprop_min_admitted" ftype="float" value='-0.5'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	170 <param name="alternative_div_amount_material" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	171 <param name="div_isotopologues_by_amount_material" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	172 <param name="isotopologues_preview" ftype="boolean" value='false'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	173 <param name="fractions_stomp_values" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	174 <param name="subtract_blankavg" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	175 <param name="under_detection_limit_set_nan" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	176 </section>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	177 <output file="isotopologuesCorrValues.tsv" name="isotopologuesCorrValues" ftype="tabular"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	178 </test>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	179 <test expect_num_outputs="3">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	180 <param name="labeled_metabo_file" ftype="xlsx" value="TRACER_metabo_4.xlsx"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	181 <param name="sample_metadata_path" ftype="tabular" value="sampleMetadata_4.csv"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	182 <param name="type_of_file_selector" value="VIBMEC_xlsx"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	183 <section name="advanced_options">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	184 <param name="isosprop_min_admitted" ftype="float" value='-0.5'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	185 <param name="alternative_div_amount_material" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	186 <param name="div_isotopologues_by_amount_material" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	187 <param name="isotopologues_preview" ftype="boolean" value='false'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	188 <param name="fractions_stomp_values" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	189 <param name="subtract_blankavg" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	190 <param name="under_detection_limit_set_nan" ftype="boolean" value='true'/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	191 </section>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	192 <output file="rawAbundances.tsv" name="rawAbundances" ftype="tabular"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	193 <output file="CorrectedIsotopologues.tsv" name="CorrectedIsotopologues" ftype="tabular"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	194 <output file="FracContribution_C.tsv" name="FracContribution_C" ftype="tabular"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	195 </test>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	196 </tests>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	197 <help><![CDATA[
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	198 TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the tabular files which are ready for DIMet tool.
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	199
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	200 Currently, the following input formats of Tracer (or Isotope-labeled) metabolomics measurements files are accepted:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	201
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	202 - IsoCor results (.tsv measurments file).
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	203 - The dataMatrix with variableMetadata ("rule" format for TraceGroomer).
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	204 - A 'generic' .xlsx measurements file, manually set by the user.
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	205 - Results provided by the VIB Metabolomics Expertise Center.
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	206
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	207 For any type of these supported inputs, TraceGroomer generates an independent file for: i) total metabolite abundances ii) Isotopologues iii) Isotopologues' proportions and iv) mean enrichment (a.k.a fractional contributions). When only Isotopologues' absolute values are provided, TraceGroomer generates all the other quantifications automatically!
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	208
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	209 Fast, automatic formatting is performed, as well as the normalisation chosen by the user: whether by the amount of material and/or by an internal standard. Useful advanced options are offered.
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	210
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	211 Note : this script does not correct for naturally occurring isotopologues. Your data must be already processed by another software that performs such correction (e.g. IsoCor, or another).
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	212
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	213
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	214 IsoCor results as input
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	215
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	216 A typical IsoCor results file is described in: https://isocor.readthedocs.io/en/latest/tutorials.html#output-files It consists of a .tsv file which has in columns the sample, metabolite, isotopologue and all quantifications, and the rows are in piled version (the samples are repeated vertically).
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	217
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	218 Our script transforms specific columns of that file into tables. As the total metabolite abundance column is not present in the input data, the total abundance per metabolite is the automatic result of the sum, per metabolite, of Isotopologues' absolute values (see AbundanceCorrected below). So here the correspondances:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	219
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	220 ================================ ========================================
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	221 column in the IsoCor file TraceGroomer output filename
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	222 ================================ ========================================
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	223 corrected_area IsotopologuesAbsolute
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	224 isotopologue_fraction IsotopologuesProportions
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	225 mean_enrichment MeanEnrichment
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	226 - AbundanceCorrected
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	227 ================================ ========================================
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	228
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	229 We provide the downloadable example from https://zenodo.org/records/10826303
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	230
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	231
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	232 The "rule" input format
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	233
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	234 This corresponds to the set of "dataMatrix", "variableMetadata", and sample metadata files. Note that the last one is required for any input format, so its explanation is given in the section "Metadata File Information".
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	235
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	236 The "dataMatrix" contains isotopologues absolute values organised in a tabular format, having a first column with the isotopologue unique identifiers and the "ID" header, whereas the sample names constitute the header of the rest of the columns. This means that isotopologues represent the rows, and samples represent the columns. The isotopologue identifiers must be unique. Example of a "dataMatrix" file:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	237
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	238 ====== ========= ========= ========= =========
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	239 ID sampleA1 sampleA2 sampleB1 sampleB2
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	240 ====== ========= ========= ========= =========
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	241 Peak1 0.54406 0.5299 0.6076 0.9352
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	242 Peak2 0.2715 0.3129 0.3139 0.0507
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	243 Peak3 0.1844 0.1571 0.0784 0.0142
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	244 ====== ========= ========= ========= =========
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	245
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	246 The "variableMetadata" provides at least three compulsory columns: ID (isotopologue unique identifiers), metabolite_name (metabolite annotation or chemical formula, being non-unique entries), and the number of labeled atoms as integer numbers. Example:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	247
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	248 ======== ================= ================
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	249 ID metabolite_name isotope_numeric
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	250 ======== ================= ================
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	251 Peak1 Acetyl_CoA 0
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	252 Peak2 Acetyl_CoA 1
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	253 Peak3 Acetyl_CoA 2
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	254 ======== ================= ================
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	255
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	256
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	257 All these files must be in tab delimited .tsv format. We provide the downloadable example from Zenodo (https://zenodo.org/records/10826303).
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	258
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	259
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	260 Note that when using this input, Tracegroomer automatically generates all the derived metrics (mean enrichment, isotopologue proportions, total abundances).
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	261
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	262
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	263 Other input formats
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	264
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	265
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	266 Please visit https://github.com/cbib/TraceGroomer/wiki/3-Supported-input-formats to get information about:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	267 - A 'generic' .xlsx measurements file, manually set by the user.
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	268 - Results provided by the VIB Metabolomics Expertise Center (El-Maven results are shaped by VIB MEC team into a multi-sheet .xlsx file).
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	269
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	270
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	271
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	272 For any type of input formats mentioned above, a samples' metadata file must be provided (section "Metadata File Information").
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	273
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	274
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	275 Metadata File Information
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	276
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	277 Provide a tab-separated file that has the names of the samples in the first column and one header row.
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	278 Column names must be exactly in this order:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	279
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	280 name_to_plot
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	281 condition
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	282 timepoint
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	283 timenum
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	284 compartment
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	285 original_name
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	286
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	287 Example Metadata File:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	288
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	289
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	290 ==================== =============== ============= ============ ================ =================
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	291 name_to_plot condition timepoint timenum compartment original_name
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	292 -------------------- --------------- ------------- ------------ ---------------- -----------------
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	293 Control_cell_T0-1 Control T0 0 cell MCF001089_TD01
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	294 Control_cell_T0-2 Control T0 0 cell MCF001089_TD02
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	295 Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	296 Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	297 Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	298 Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	299 Control_med_T24-1 Control T24 24 med MCF001090_TD02
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	300 Control_med_T24-2 Control T24 24 med MCF001090_TD03
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	301 Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	302 Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	303 Control_med_T0-1 Control T0 0 med MCF001090_TD06
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	304 Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	305 ==================== =============== ============= ============ ================ =================
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	306
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	307
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	308 The column original_name must have the names of the samples as given in your data.
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	309
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	310 The column name_to_plot must have the names as you want them to be (or set identical to original_name if you prefer). To set names that
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	311 are meaningful is a better choice, as we will take them to display the results.
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	312
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	313 The column timenum must contain only the numeric part of the timepoint, for example 2,0, 10, 100 (this means, without letters ("T", "t", "s", "h" etc)
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	314 nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!).
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	315
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	316 The column compartment is an abbreviation, coined by you, for the compartments. This will be used for the results' files names: the longer the
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	317 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column.
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	318
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	319
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	320 Advanced options
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	321
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	322 These options allow the user to:
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	323
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	324 - Normalize by the amount of material (number of cells, tissue weight): the user must provide a tab delimited file, with a header, having the first column with the same names as in metadata 'original_name', and the second column the quantitative information, without zeroes nor negative numbers.
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	325 - Normalize by an internal standard (present in your data) at choice.
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	326 - Print a preview of isotopologues values.
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	327
1 c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2 iuc parents: 0 diff changeset	328 Please visit our Wiki page (https://github.com/cbib/TraceGroomer/wiki) for more information, and how to get help. Details of advanced options available in https://github.com/cbib/TraceGroomer/wiki/4-Advanced-options.
0 5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	329
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	330 ]]>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	331 </help>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	332 <expand macro="citations" />
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32 iuc parents: diff changeset	333 </tool>

Mercurial > repos > iuc > tracegroomer

annotate tracegroomer.xml @ 1:c6a7bbc6066d draft default tip