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comparison tracegroomer.xml @ 1:c6a7bbc6066d draft default tip

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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
comparison
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0:5f7d672647b0 1:c6a7bbc6066d
35 $div_isotopologues_by_amount_material 35 $div_isotopologues_by_amount_material
36 $isotopologues_preview 36 $isotopologues_preview
37 $fractions_stomp_values 37 $fractions_stomp_values
38 $subtract_blankavg 38 $subtract_blankavg
39 $under_detection_limit_set_nan 39 $under_detection_limit_set_nan
40 -ox 'tsv' && 40 -ox $output_files_extension &&
41 #if $type_of_file.type_of_file_selector == "IsoCor_out_tsv": 41 #if $type_of_file.type_of_file_selector == "IsoCor_out_tsv":
42 cp -rf '${AbundanceCorrected}.tsv' '${AbundanceCorrected}' && 42 cp -rf '${AbundanceCorrected}.${output_files_extension}' '${AbundanceCorrected}' &&
43 cp -rf '${MeanEnrichment13C}.tsv' '${MeanEnrichment13C}' && 43 cp -rf '${MeanEnrichment13C}.${output_files_extension}' '${MeanEnrichment13C}' &&
44 cp -rf '${IsotopologuesProp}.tsv' '${IsotopologuesProp}' && 44 cp -rf '${IsotopologuesProp}.${output_files_extension}' '${IsotopologuesProp}' &&
45 cp -rf '${IsotopologuesAbs}.tsv' '${IsotopologuesAbs}' 45 cp -rf '${IsotopologuesAbs}.${output_files_extension}' '${IsotopologuesAbs}'
46 #else if $type_of_file.type_of_file_selector == "rule_tsv": 46 #else if $type_of_file.type_of_file_selector == "rule_tsv":
47 cp -rf '${Absolute_isotopologue_abundances}.tsv' '${Absolute_isotopologue_abundances}' 47 cp -rf '${Absolute_isotopologue_abundances}.${output_files_extension}' '${Absolute_isotopologue_abundances}'
48 #else if $type_of_file.type_of_file_selector == "generic_xlsx": 48 #else if $type_of_file.type_of_file_selector == "generic_xlsx":
49 cp -rf '${sheetname}.tsv' '${isotopologuesCorrValues}' 49 cp -rf '${sheetname}.${output_files_extension}' '${isotopologuesCorrValues}'
50 #else: 50 #else:
51 cp -rf '${raw_abundance_sheet_name}.tsv' '${rawAbundances}' && 51 cp -rf '${raw_abundance_sheet_name}.${output_files_extension}' '${rawAbundances}' &&
52 cp -rf '${frac_contribution_sheet_name}.tsv' '${FracContribution_C}' && 52 cp -rf '${frac_contribution_sheet_name}.${output_files_extension}' '${FracContribution_C}' &&
53 cp -rf '${corrected_isotopologues_sheet_name}.tsv' '${CorrectedIsotopologues}' 53 cp -rf '${corrected_isotopologues_sheet_name}.${output_files_extension}' '${CorrectedIsotopologues}'
54 #end if 54 #end if
55 55
56 ]]></command> 56 ]]></command>
57 57
58 <configfiles> 58 <configfiles>
96 <inputs> 96 <inputs>
97 <expand macro="input_datasets"/> 97 <expand macro="input_datasets"/>
98 <expand macro="advanced_options"/> 98 <expand macro="advanced_options"/>
99 </inputs> 99 </inputs>
100 <outputs> 100 <outputs>
101 <data label="Corrected isotope abundances" name="AbundanceCorrected" format="tabular"> 101 <data label="Total metabolite abundances" name="AbundanceCorrected" format="tabular">
102 <filter>type_of_file['type_of_file_selector'] == 'IsoCor_out_tsv'</filter> 102 <filter>type_of_file['type_of_file_selector'] == 'IsoCor_out_tsv'</filter>
103 </data> 103 </data>
104 <data label="Mean enrichment data" name="MeanEnrichment13C" format="tabular"> 104 <data label="Mean enrichment data" name="MeanEnrichment13C" format="tabular">
105 <filter>type_of_file['type_of_file_selector'] == 'IsoCor_out_tsv'</filter> 105 <filter>type_of_file['type_of_file_selector'] == 'IsoCor_out_tsv'</filter>
106 </data> 106 </data>
131 <param name="labeled_metabo_file" ftype="tabular" value="TRACER_IsoCor_out_example.tsv"/> 131 <param name="labeled_metabo_file" ftype="tabular" value="TRACER_IsoCor_out_example.tsv"/>
132 <param name="sample_metadata_path" ftype="tabular" value="sampleMetadata_1.csv"/> 132 <param name="sample_metadata_path" ftype="tabular" value="sampleMetadata_1.csv"/>
133 <param name="type_of_file_selector" value="IsoCor_out_tsv"/> 133 <param name="type_of_file_selector" value="IsoCor_out_tsv"/>
134 <section name="advanced_options"> 134 <section name="advanced_options">
135 <param name="isosprop_min_admitted" ftype="float" value='-0.5'/> 135 <param name="isosprop_min_admitted" ftype="float" value='-0.5'/>
136 <param name="alternative_div_amount_material" ftype="boolean" value='true'/> 136 <param name="alternative_div_amount_material" ftype="boolean" value='true'/>
137 <param name="div_isotopologues_by_amount_material" ftype="boolean" value='true'/> 137 <param name="div_isotopologues_by_amount_material" ftype="boolean" value='true'/>
138 <param name="isotopologues_preview" ftype="boolean" value='false'/> 138 <param name="isotopologues_preview" ftype="boolean" value='false'/>
139 <param name="fractions_stomp_values" ftype="boolean" value='true'/> 139 <param name="fractions_stomp_values" ftype="boolean" value='true'/>
140 <param name="subtract_blankavg" ftype="boolean" value='true'/> 140 <param name="subtract_blankavg" ftype="boolean" value='true'/>
141 <param name="under_detection_limit_set_nan" ftype="boolean" value='true'/> 141 <param name="under_detection_limit_set_nan" ftype="boolean" value='true'/>
142 </section> 142 </section>
143 <output file="AbundanceCorrected.tsv" name="AbundanceCorrected" ftype="tabular"/> 143 <output file="AbundanceCorrected.tsv" name="AbundanceCorrected" ftype="tabular"/>
144 <output file="IsotopologuesAbs.tsv" name="IsotopologuesAbs" ftype="tabular"/> 144 <output file="IsotopologuesAbs.tsv" name="IsotopologuesAbs" ftype="tabular"/>
145 <output file="IsotopologuesProp.tsv" name="IsotopologuesProp" ftype="tabular"/> 145 <output file="IsotopologuesProp.tsv" name="IsotopologuesProp" ftype="tabular"/>
323 323
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. 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.
325 - Normalize by an internal standard (present in your data) at choice. 325 - Normalize by an internal standard (present in your data) at choice.
326 - Print a preview of isotopologues values. 326 - Print a preview of isotopologues values.
327 327
328 Please visit our Wiki page (https://github.com/cbib/TraceGroomer/wiki) for more information, and how to get help. 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.
329 329
330 ]]> 330 ]]>
331 </help> 331 </help>
332 <expand macro="citations" /> 332 <expand macro="citations" />
333 </tool> 333 </tool>