Add tracegroomer tool

tools/tracegroomer/.shed.yml

@@ -0,0 +1,15 @@
+categories:
+- Metabolomics
+description: TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.
+homepage_url: https://github.com/cbib/TraceGroomer
+long_description: 'TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.'
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for Tracegroomer application {{ tool_name }}."
+suite:
+  name: "suite_tra"
+  description: "TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .tsv files which are ready for DIMet tool."
+  type: repository_suite_definition

tools/tracegroomer/macros.xml

@@ -0,0 +1,109 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">tracegroomer</requirement>
+        </requirements>
+    </xml>
+    <xml name="input_datasets">
+        <param name="labeled_metabo_file" type="data" optional="false" format="tabular,xlsx" label="Labeled metabolomics file"/>
+        <param name="sample_metadata_path" type="data" format="tabular" label="sample metadata file" help="The metadata, a unique file with the description of the samples in your measures files. This is compulsory, see section Metadata File Information."/>
+        <param name="amount_material" type="data" optional="true" format="interval" label="amount material" help="file having the amount of material (number of cells, tissue weight, etc) by sample, for the normalization"/>
+        <param name="remove_these_metabolites" type="data" optional="true" format="interval" label="remove metabolites using this file" help="Absolute path to the file with columns:  compartment, metabolite; listing the metabolites to be completely excluded (you know what you are doing)"/>
+        <conditional name="type_of_file">
+            <param name="type_of_file_selector" type="select" label="Choose which type of input file is used" help="One of the following: IsoCor_out_tsv|rule_tsv|VIBMEC_xlsx|generic_xlsx">
+                    <option value="IsoCor_out_tsv" selected="true">isocor output file</option>
+                    <option value="VIBMEC_xlsx">VIBMEC xlsx file</option>
+                    <option value="generic_xlsx">generic xlsx file</option>
+                    <option value="rule_tsv">rule tsv file</option>
+            </param>
+            <when value="IsoCor_out_tsv">
+            </when>
+            <when value="generic_xlsx">
+                <param name="sheetname" type="text" value="isotopologuesCorrValues" optional="false" label="name of the sheet containing the isotopologues corrected values" >
+                        <sanitizer invalid_char="">
+                            <valid initial="string.ascii_letters,string.digits">
+                                <add value="_" />
+                            </valid>
+                        </sanitizer>
+                    </param>
+            </when>
+            <when value="VIBMEC_xlsx">
+                <param name="raw_abundance_sheet_name" type="text" value="rawAbundances" optional="false" label="name of the sheet containing the raw abundances values" >
+                        <sanitizer invalid_char="">
+                            <valid initial="string.ascii_letters,string.digits">
+                                <add value="_" />
+                            </valid>
+                        </sanitizer>
+                </param>
+                <param name="frac_contribution_sheet_name" type="text" value="FracContribution_C" optional="false" label="name of the sheet containing the mean enrichment  values" >
+                        <sanitizer invalid_char="">
+                            <valid initial="string.ascii_letters,string.digits">
+                                <add value="_" />
+                            </valid>
+                        </sanitizer>
+                </param>
+                <param name="corrected_isotopologues_sheet_name" type="text" value="CorrectedIsotopologues" optional="false" label="name of the sheet containing the isotopologues corrected values" >
+                        <sanitizer invalid_char="">
+                            <valid initial="string.ascii_letters,string.digits">
+                                <add value="_" />
+                            </valid>
+                        </sanitizer>
+                </param>
+            </when>
+            <when value="rule_tsv">
+                <param name="variable_metadata_path" type="data" format="tabular" label="variable metadata file" help="The metadata, a unique file with the description of the samples in your measures files. This is compulsory, see section Metadata File Information."/>
+                <section name="columns_variable_metadata_description" title="variable metadata file columns description" expanded="false">
+                    <param name="identifier" type="text" value="ID" optional="false" label="identifier of your metabolite in variable metadata file" >
+                        <sanitizer invalid_char="">
+                            <valid initial="string.ascii_letters,string.digits">
+                                <add value="_" />
+                            </valid>
+                        </sanitizer>
+                    </param>
+                    <param name="compound" type="text" value="metabolite_name" optional="false" label="name of your metabolite in variable metadata file (formula is also accepted)" >
+                        <sanitizer invalid_char="">
+                            <valid initial="string.ascii_letters,string.digits">
+                                <add value="_" />
+                            </valid>
+                        </sanitizer>
+                    </param>
+                    <param name="isotopologue_number" value="isotope_numeric" type="text" optional="false" label="isotopologue number in variable metadata file" >
+                        <sanitizer invalid_char="">
+                            <valid initial="string.ascii_letters,string.digits">
+                                <add value="_" />
+                            </valid>
+                        </sanitizer>
+                    </param>
+                </section>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="advanced_options">
+        <section name="advanced_options" title="Advanced options" expanded="false">
+            <param name="alternative_div_amount_material" type="boolean" value="true" label="add strip plot on abundance bar" help="When dividing values by the amount of material, also multiplies by mean(amountMaterial) to stay in abundance units"/>
+            <param name="div_isotopologues_by_amount_material" type="boolean" value="true" label="isotopologues by amount material" help="Apply normalization by the amount of material, at the level of isotopologue absolute values. After this, re-computes all derived metrics. If False, only total abundances are normalized"/>
+            <param name="use_internal_standard" type="text" optional="true" help="Internal Standard for performing the division: abundances/internal_standard, example: --use_internal_standard Myristic_acid_d27. By default is not performed." label="internal standard" />
+            <param name="isotopologues_preview" type="boolean" value="false" label="Plot isotopologue" help="Plot isotopologue values, as given"/>
+            <param name="isosprop_min_admitted" type="float" min="-1.0" max="1.0" value="-0.5" label="isotopologues cutoff" help="Metabolites whose isotopologues proportions are less or equal to this cutoff, are removed"/>
+            <param name="fractions_stomp_values" type="boolean" value="true" label="Stomps fractional contributions" help="Stomps fractional contributions (synonym: mean enrichment), and isotopologue proportions, to max 1.0 and min 0.0"/>
+            <param name="under_detection_limit_set_nan" type="boolean" value="true" label="Limit Of Detection" help="On VIB results. Any abundance inferior to LOD (Limit Of Detection), is set as NaN"/>
+            <param name="subtract_blankavg" type="boolean" value="true" label="" help="On VIB results. From samples abundances,  subtracts the average of the blanks"/>
+        </section>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @software{Galvis_Rodriguez_DIMet,
+                    author = {Galvis Rodriguez, Johanna  and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha},
+                    license = {MIT},
+                    title = {{DIMet}},
+                    url = {https://github.com/cbib/DIMet}
+                    }
+
+            </citation>
+        </citations>
+
+    </xml>
+</macros>

tools/tracegroomer/test-data/Absolute_isotopologue_abundances.tsv

@@ -0,0 +1,24 @@
+ID	A_T0_endo-1	A_T0_endo-2	Cont_T0_endo-1	Cont_T0_endo-2	A_T24_endo-1	A_T24_endo-2	Cont_T24_endo-1	Cont_T24_endo-2	A_T0_exo-1	A_T0_exo-2	Cont_T0_exo-1	Cont_T0_exo-2	A_T24_exo-1	A_T24_exo-2	Cont_T24_exo-1	Cont_T24_exo-2
+2-OHGLu_m+0	5550339.322	6072872.833	5893256.269	7454336.274	3855047.791	3216178.72		4066632.965	5550339.322	6072872.833	5893256.269	7454336.274	3855047.791	3216178.72	3102049.195	4066632.965
+2-OHGLu_m+1	0.0	0.0	0.0	0.0	0.0	0.0		0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
+2-OHGLu_m+2	62163.30727	108839.8963	9976.217534	53035.94662	3114533.603	2691689.195		1611494.416	62163.30727	108839.8963	9976.217534	53035.94662	3114533.603	2691689.195	1845577.773	1611494.416
+2-OHGLu_m+3	33950.03875	57015.80123	16218.60873	34068.8323	964673.6406	804919.6602		479959.6627	33950.03875	57015.80123	16218.60873	34068.8323	964673.6406	804919.6602	474922.8927	479959.6627
+2-OHGLu_m+4	31513.15643	43506.47502	18965.84568	23046.25122	5436469.924	4706821.45		2732129.436	31513.15643	43506.47502	18965.84568	23046.25122	5436469.924	4706821.45	3200529.756	2732129.436
+2-OHGLu_m+5	27688.74195	43567.73063	0.0	17896.32501	2769721.539	2302254.26		1298081.886	27688.74195	43567.73063	0.0	17896.32501	2769721.539	2302254.26	1488534.123	1298081.886
+2_3-PG_m+0	206171.4626	285834.0353	298441.8262	268050.3636	36413.27637	27367.17784	26381.30429	23698.7623	206171.4626	285834.0353	298441.8262	268050.3636	36413.27637	27367.17784	26381.30429	23698.7623
+2_3-PG_m+1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
+2_3-PG_m+2	133780.182	161461.2364	200778.0533	197229.6694	182631.3947	132170.3807	146120.9923	89966.23931	133780.182	161461.2364	200778.0533	197229.6694	182631.3947	132170.3807	146120.9923	89966.23931
+2_3-PG_m+3	8358749.348	10271010.45	11787744.65	11554464.86	10505228.3	8376820.028	9033424.374	6122480.462	8358749.348	10271010.45	11787744.65	11554464.86	10505228.3	8376820.028	9033424.374	6122480.462
+6-PG_m+0	309932.3475	342540.1698	253560.3827	242260.6594	101608.1805	84940.35902	85240.79781	67359.24717	309932.3475	342540.1698	253560.3827	242260.6594	101608.1805	84940.35902	85240.79781	67359.24717
+6-PG_m+1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
+6-PG_m+2	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
+6-PG_m+3	7664.136895	8906.391308	0.0	0.0	0.0	0.0	0.0	0.0	7664.136895	8906.391308	0.0	0.0	0.0	0.0	0.0	0.0
+6-PG_m+4	11950.01113	11674.22491	9922.705217	15475.23458	45346.04708	36334.93958	34524.35854	26037.70094	11950.01113	11674.22491	9922.705217	15475.23458	45346.04708	36334.93958	34524.35854	26037.70094
+6-PG_m+5	520904.6672	608128.1002	405342.3913	815587.5165	2390706.721	1802278.633	1807036.326	1207909.718	520904.6672	608128.1002	405342.3913	815587.5165	2390706.721	1802278.633	1807036.326	1207909.718
+6-PG_m+6	7423820.948	8341569.748	5394323.444	7384800.665	15231875.3	12525321.98	11279297.92	8040213.605	7423820.948	8341569.748	5394323.444	7384800.665	15231875.3	12525321.98	11279297.92	8040213.605
+a-KG_m+0	441807.2042	612669.4773	552526.6043	482434.0877	1476617.063	1056307.521	572619.741	546375.578	441807.2042	612669.4773	552526.6043	482434.0877	1476617.063	1056307.521	572619.741	546375.578
+a-KG_m+1	6581.125045	12456.03716	0.0	2085.213699	77677.31383	46821.38405	28170.23998	32113.8241	6581.125045	12456.03716	0.0	2085.213699	77677.31383	46821.38405	28170.23998	32113.8241
+a-KG_m+2	70778.42058	118643.5176	46309.55877	54983.84668	1907292.33	1596531.466	636158.2851	415566.8382	70778.42058	118643.5176	46309.55877	54983.84668	1907292.33	1596531.466	636158.2851	415566.8382
+a-KG_m+3	22143.37798	32170.99354	13728.65106	12489.92256	623361.4049	483118.3355	149649.632	103268.9093	22143.37798	32170.99354	13728.65106	12489.92256	623361.4049	483118.3355	149649.632	103268.9093
+a-KG_m+4	21225.1587	33085.30969	9561.259531	10809.82522	3267732.931	2762185.304	1099424.672	647876.2431	21225.1587	33085.30969	9561.259531	10809.82522	3267732.931	2762185.304	1099424.672	647876.2431
+a-KG_m+5	0.0	0.0	0.0	0.0	1721462.381	1381372.254	489385.3877	299919.5187	0.0	0.0	0.0	0.0	1721462.381	1381372.254	489385.3877	299919.5187

tools/tracegroomer/test-data/AbundanceCorrected.tsv

@@ -0,0 +1,39 @@
+ID	T0_A_1	T0_A_2	T24_A_1	T24_A_2
+2_3-PG	8698700.9926	10718305.7217	10724272.97107	8536357.58654
+2-OHGLu	5705654.5664	6325802.73618	16140446.4976	13721863.2852
+6-PG	8274272.110725	9312818.634218	17769536.24858	14448875.911600001
+a-KG	562535.286505	809025.3352900001	9074143.42373	7326336.2645499995
+Cit	6104076.527709001	6622207.696758	17362710.7065	15099558.4283
+Fru6P	4798767.932639999	4513233.6544699995	4837930.1953	3290337.21892
+FruBP	38638958.584489994	35926915.2997	15919121.42811	12742908.812899
+Fru1P	8649509.40162	9221146.82622	7263530.71345	6382941.54406
+Fum	849934.584649	1331932.8614599998	2536771.76908	2002385.5281600002
+Glc6P	1371473.29828	1417858.38996	2378469.26438	1566613.8815600001
+Gly3P	2279532.84135	1472280.30519	2323362.4118999997	1159698.9703000002
+IsoCit	686751.7917999999	765537.5006919999	1173628.11465	958226.4224050001
+Mal	16359379.550800001	21696115.306900002	30979835.452200003	28483388.116600007
+P5P	1622226.252397	2101779.62568	4042496.89333	2745142.88324
+PEP	372560.40297	389149.56301800004	901546.463227	300696.507413
+PRPP	3265374.30386	1403175.78537	4685589.198954	1127901.1055990001
+Pyr	8072604.6678	5417572.18565	19414603.972400002	10572949.759383999
+Rib1P	506931.49994	515317.83285	1058757.54637	600209.415023
+Sed7P	405451.02691599994	404632.682093	4256316.13784	3311139.573476
+Suc	16696697.2474	24960174.386	15430602.704	19913145.336999997
+ADP	34025169.109877	37691400.360171005	37723605.076560006	32519284.07825
+AMP	9565403.92	9556049.635	7405683.36312	5000743.872590001
+ATP	41541098.171906	28333872.96799	43782778.395509996	24613580.795915
+CDP	3658703.167	4549519.711	2782262.726477	2433762.26766
+CMP	2104346.331	1898991.26	1261049.8005600001	716871.07791
+CTP	11009149.04	9279476.88	9892652.365619998	6630162.09119
+GDP	9123811.404098999	9618774.8438531	9949031.84874	7448744.72431
+GMP	1040843.97418	983805.82424	955450.71251	624256.36527
+GTP	12846360.211278	8724055.649473	11838142.32576	4862598.134269999
+UDP	19095395.197940003	22041850.9617	26939623.55273	25193602.076109998
+UMP	29113743.746113002	27845070.620795995	31071457.37046	23274629.08901
+UTP	37904488.04698	32947660.03249	41928292.11218999	30037598.8316
+Glutamate	8642056.8426	17149266.2103	47245553.7829	42301398.0359
+Alanine	26433669.23424036	29757276.54221551	114131556.02470112	105304217.6372259
+Aspartate	4153600.4715071535	23560016.546284568	20479103.26962672	28642684.62216362
+Glutamine	15391319.615471464	49113624.6255005	35714798.47397325	26092787.779812228
+Glycine	354765284.35181	292769623.48668975	574309132.522843	468271969.5574398
+Serine	773712972.5683433	1423520249.5635524	1965385721.033115	1753994669.6276615