initial commit

tools/influx_data_manager/.shed.yml

@@ -0,0 +1,5 @@
+name: physiofit_manager
+owner: workflow4metabolomics
+description: Handling of physiofit input files
+categories: [Metabolomics]
+homepage_url: https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/

tools/influx_data_manager/influx_data_manager.xml

@@ -0,0 +1,82 @@
+<tool id="influx_data_manager" name="Influx Data Manager: Handling influx_si data inputs in Galaxy workflows" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+    <macros>
+        <token name='@TOOL_VERSION@'>1.0.0</token>
+    </macros>
+    <requirements>
+        <requirement type='package' version='@TOOL_VERSION@'>influx-si-data-manager</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    influx_data_manager
+    --physiofit $in_physiofit 
+    --isocor $in_isocor 
+    --linp $in_linp 
+    --netw $in_netw 
+    --mmet $in_mmet 
+    --cnstr $in_cnstr 
+    --tvar $in_tvar 
+    --opt $in_opt 
+    --log $out_log
+    #if $verbose == 'true':
+        -v
+    #end if 
+    2> $err_out
+    ]]></command>
+    <inputs>
+        <param type='data' name='in_netw' label='netw' help='File containing network for experiments (.netw file)' optional='false'/>
+        <param type='data' name='in_isocor' label='miso' help='Output of isocor which corresponds to the .miso input' optional='false'/>
+        <param type='data' name='in_tvar' label='tvar' help='File containing types of variables for experiments (.tvar file)' optional='false'/>
+        <param type='data' name='in_physiofit' label='mflux' help='Output of physiofit which corresponds to the .mflux input' optional='true'/>
+        <param type='data' name='in_linp' label='linp' help='File contianing label inputs for experiments (.linp file)' optional='true'/>
+        <param type='data' name='in_mmet' label='mmet' help='File containing specie concentrations for experiments (.mmet file)' optional='true'/>
+        <param type='data' name='in_cnstr' label='cnstr' help='File containing constraints onf fluxes and specie concentrations for experiments (.constr file)' optional='true'/>
+        <param type='data' name='in_opt' label='opt' help='File containing options for influx_si (.opt  file)' optional='true'/>
+        <param name='verbose' type='select' label='Debug mode' help='Select "Yes" to have debug logs be printed out'>
+            <option value='true'>Yes</option>
+            <option value='false'>No</option>
+        </param>     
+    </inputs>
+    <outputs>
+        <data format='txt' name='out_log' label='Run log'/>
+        <collection type='list' label='Influx_si input files' name='list_output'>
+            <discover_datasets pattern='__name_and_ext__' format='zip'/>
+        </collection>
+        <data format='txt' name='err_out' label='Influx DM error log'/>
+    </outputs>
+    <tests>
+        <test>
+            <param name='in_netw' value='galaxy_test.netw'/>
+            <param name='in_isocor' value='galaxy_test.tsv'/>
+            <param name='in_tvar' value='galaxy_test.tvar'/>
+            <param name='in_physiofit' value='galaxy_test.csv'/>
+            <param name='in_linp' value='galaxy_test.linp'/>
+            <!-- <param name='in_mmet' value='galaxy_test.mmet'/> FOR FUTURE USE IN INSTATIONARY SETTING -->
+            <param name='in_cnstr' value='galaxy_test.cnstr'/>
+            <param name='in_opt' value='galaxy_test.opt'/>
+            <param name='verbose' value='true'/>
+            <output_collection name='list_output' type='list'>
+                <element name='Sample_1'>
+                    <assert_contents>
+                        <has_archive_member path='Sample_1.miso'/>
+                        <has_archive_member path='Sample_1.mflux'/>
+                        <has_archive_member path='Sample_1.netw'/>
+                        <has_archive_member path='Sample_1.tvar'/>
+                        <has_archive_member path='Sample_1.linp'/>
+                        <has_archive_member path='Sample_1.cnstr'/>
+                        <has_archive_member path='Sample_1.opt'/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+    This tool is mean to handle the input files for influx_si within workflows. It is not meant to be used as a stand-alone within the platform.
+    ]]></help>
+    <citations>
+        <citation type='bibtex'>
+    @misc{githubinflux_si,
+      author = {Le Gregam, Loic},
+      year = {2024},
+      title = {Influx-si-data-manager},
+    }</citation>
+        </citations>
+</tool>

tools/influx_data_manager/test-data/galaxy_test.cnstr

@@ -0,0 +1,14 @@
+# Created by 'ftbl2mtf e_coli.ftbl -o mtf/' at 2022-05-25 17:04:34 CEST +0200
+Id	Comment	Kind	Formula	Operator	Value
+		NET	fum_a-fum_b	==	0
+		NET	Glucupt_1+Glucupt_U	==	1
+		NET	bs_oaa3a-bs_oaa3b	==	0
+		NET	bs_pep3a-bs_pep3b	==	0
+		NET	bs_pep4a-bs_pep4b	==	0
+		XCH	fum_a-fum_b	==	0
+		NET	pyk	>=	1
+		NET	edd	>=	0.0001
+		NET	gnd	>=	0.0001
+		NET	zwf	>=	0.0001
+		NET	ppc	>=	0.0001
+		NET	mae	>=	0.0001

tools/influx_data_manager/test-data/galaxy_test.csv

@@ -0,0 +1,7 @@
+experiments,parameter name,optimal,mean,sd,median,CI_2.5,CI_97.5
+Sample_1,X_0,0.0329312189290397,0.03273713313662519,0.007609017703709359,0.03219318489769323,0.020658517746097546,0.04736453335848851
+Sample_1,growth_rate,0.5383433996018128,0.5395703238461335,0.04102569335782071,0.5394601977232022,0.4613085770850412,0.6201562744358701
+Sample_1,Glc_q,-6.419870665015181,-6.650785988032335,1.044024329080937,-6.498027583698613,-9.17532462567154,-5.222667405151508
+Sample_1,Glc_M0,14.159111013782852,14.147486873533602,0.1551536419173369,14.138190672983116,13.83041251171807,14.421108697615226
+Sample_1,Ace_q,2.4805506633403795,2.595699697613964,0.4296293828448397,2.557842469095964,1.9706068793983569,3.701359051903215
+Sample_1,Ace_M0,0.15516855130543258,0.1415870343951678,0.09293014893700775,0.13950478764426216,1e-06,0.34673234203889314

tools/influx_data_manager/test-data/galaxy_test.linp

@@ -0,0 +1,6 @@
+# Created by 'ftbl2mtf e_coli.ftbl -o mtf/' at 2022-05-25 17:04:34 CEST +0200
+Id	Comment	Specie	Isotopomer	Value
+		Gluc_U	111111	1
+		Gluc_U	000000	0.
+		Gluc_1	100000	1.
+		Gluc_1	000000	0.

tools/influx_data_manager/test-data/galaxy_test.netw

@@ -0,0 +1,87 @@
+# Created by 'ftbl2mtf e_coli.ftbl -o mtf/' at 2022-05-25 17:04:34 CEST +0200
+Glucupt_1:	Gluc_1 (ABCDEF) -> Glc6P (ABCDEF)
+Glucupt_U:	Gluc_U (ABCDEF) -> Glc6P (ABCDEF)
+pgi:	Glc6P (ABCDEF) <-> Fru6P (ABCDEF)
+pfk:	Fru6P (ABCDEF) -> FruBP (ABCDEF)
+ald:	FruBP (ABCDEF) <-> GA3P (CBA) + GA3P (DEF)
+pgk:	GA3P (ABC) <-> PGA (ABC)
+eno:	PGA (ABC) <-> PEP (ABC)
+pyk:	PEP (ABC) <-> Pyr (ABC)
+zwf:	Glc6P (ABCDEF) -> Gnt6P (ABCDEF)
+gnd:	Gnt6P (ABCDEF) -> CO2 (A) + Rib5P (BCDEF)
+edd:	Gnt6P (ABCDEF) -> Pyr (ABC) + GA3P (DEF)
+ta:	GA3P (ABC) + Sed7P (abcdefg) <-> Ery4P (defg) + Fru6P (abcABC)
+tk1:	Rib5P (ABCDE) + Rib5P (abcde) <-> GA3P (CDE) + Sed7P (ABabcde)
+tk2:	Rib5P (ABCDE) + Ery4P (abcd) <-> GA3P (CDE) + Fru6P (ABabcd)
+pdh:	Pyr (ABC) <-> AcCoA (BC) + CO2 (A)
+citsynth:	AcCoA (AB) + OAA (abcd) -> ICit (dcbaBA)
+idh:	ICit (ABCDEF) -> AKG (ABCEF) + CO2 (D)
+akgdh:	AKG (ABCDE) -> Suc (BCDE) + CO2 (A)
+fum_a:	Suc (ABCD) <-> Mal (ABCD)
+fum_b:	Suc (ABCD) <-> Mal (DCBA)
+maldh:	Mal (ABCD) <-> OAA (ABCD)
+ppc:	PEP (ABC) + CO2 (a) <-> OAA (ABCa)
+mae:	Mal (ABCD) -> Pyr (ABC) + CO2 (D)
+bs_glc6P:	Glc6P (ABCDEF) -> BM_Glc6P (ABCDEF)
+bs_fru6P:	Fru6P (ABCDEF) -> BM_Fru6P (ABCDEF)
+bs_pga:	PGA (ABC) -> BM_PGA (ABC)
+bs_pga_aux:	BM_PGA (ABC) -> PGA_Aux (ABC)
+bs_pga1:	BM_PGA (ABC) -> Ser (ABC)
+bs_pga1_aux:	Ser (ABC) -> Ser_Aux (ABC)
+bs_pga2:	Ser (ABC) -> Cys (ABC)
+bs_pga2_aux:	Cys (ABC) -> Cys_Aux (ABC)
+bs_pga3:	Ser (ABC) <-> Gly (AB) + FTHF (C)
+bs_pga3_aux:	Gly (AB) -> Gly_Aux (AB)
+bs_DHAP:	GA3P (ABC) -> Glp (ABC)
+bs_pyr:	Pyr (ABC) -> BM_Pyr (ABC)
+bs_pyr1:	BM_Pyr (ABC) -> Ala (ABC)
+bs_pyr1_aux:	Ala (ABC) -> Ala_Aux (ABC)
+bs_pyr2:	BM_Pyr (ABC) + BM_Pyr (abc) -> AKV (ABbcC) + CO2 (a)
+bs_pyr4:	AKV (ABCDE) -> Val (ABCDE)
+bs_pyr4_aux:	Val (ABCDE) -> Val_Aux (ABCDE)
+bs_pyr3:	AKV (ABCDE) + BM_AcCoA (ab) -> Leu (abBCDE) + CO2 (A)
+bs_pyr3_aux:	Leu (ABCDEF) -> Leu_Aux (ABCDEF)
+bs_e4p:	Ery4P (ABCD) -> BM_Ery4P (ABCD)
+bs_rib5p:	Rib5P (ABCDE) -> BM_Rib5P (ABCDE)
+bs_rib5p1:	BM_Rib5P (ABCDE) + FTHF (a) -> His (EDCBAa)
+bs_rib5p1_aux:	His (ABCDEF) -> His_Aux (ABCDEF)
+bs_rib5p2:	BM_Rib5P (ABCDE) -> Ri5P_Aux (ABCDE)
+bs_pep:	PEP (ABC) -> BM_PEP (ABC)
+bs_pep1:	BM_PEP (ABC) + BM_Ery4P (abcd) -> DAHP (ABCabcd)
+bs_pep2:	BM_PEP (ABC) + DAHP (abcdefg) -> Chor (ABCabcdefg)
+bs_pep3a:	Chor (ABCDEFGHIJ) -> Phe (ABCEFGHIJ) + CO2 (D)
+bs_pep3b:	Chor (ABCDEFGHIJ) -> Phe (ABCEJIHGF) + CO2 (D)
+bs_pep3_aux:	Phe (ABCEFGHIJ) -> Phe_Aux (ABCEFGHIJ)
+bs_pep4a:	Chor (ABCDEFGHIJ) -> Tyr (ABCEFGHIJ) + CO2 (D)
+bs_pep4b:	Chor (ABCDEFGHIJ) -> Tyr (ABCEJIHGF) + CO2 (D)
+bs_pep4_aux:	Tyr (ABCEFGHIJ) -> Tyr_Aux (ABCEFGHIJ)
+bs_pep5:	BM_PEP (ABC) -> PEP_Aux (ABC)
+bs_pep6:	Chor (ABCDEFGHIJ) + BM_Rib5P (abcde) -> Trp (edcbaJEFGHI) + PyrCO2 (ABCD)
+bs_pep6_aux:	Trp (ABCDEFGHIJK) -> Trp_Aux (ABCDEFGHIJK)
+bs_pep7:	PyrCO2 (ABCD) -> Pyr (ABC) + CO2 (D)
+bs_accoa:	AcCoA (AB) -> BM_AcCoA (AB)
+bs_accoa_aux:	BM_AcCoA (AB) -> AcCoA_Aux (AB)
+bs_akg:	AKG (ABCDE) -> BM_AKG (ABCDE)
+bs_akg1:	BM_AKG (ABCDE) -> Glu (ABCDE)
+bs_akg2:	Glu (ABCDE) -> Pro (ABCDE)
+bs_akg3:	Glu (ABCDE) -> Gln (ABCDE)
+bs_akg4:	Glu (ABCDE) + CO2 (a) -> Arg (ABCDEa)
+bs_akg4_aux:	Arg (ABCDEF) -> Arg_Aux (ABCDEF)
+bs_oaa:	OAA (ABCD) -> BM_OAA (ABCD)
+bs_oaa1:	BM_OAA (ABCD) -> Asp (ABCD)
+bs_oaa1_aux:	Asp (ABCD) -> Asp_Aux (ABCD)
+bs_oaa2:	Thr (ABCD) + BM_Pyr (abc) -> Ile (ABbCDc) + CO2 (a)
+bs_oaa2_aux:	Ile (ABCDEF) -> Ile_Aux (ABCDEF)
+bs_oaa3a:	BM_OAA (ABCD) + BM_Pyr (abc) -> Lys (ABCDcb) + CO2 (a)
+bs_oaa3b:	BM_OAA (ABCD) + BM_Pyr (abc) -> Lys (abcDCB) + CO2 (A)
+bs_oaa3_aux:	Lys (ABCDEF) -> Lys_Aux (ABCDEF)
+bs_oaa4:	BM_OAA (ABCD) -> OAA_Aux (ABCD)
+bs_oaa5:	BM_OAA (ABCD) -> Thr (ABCD)
+bs_oaa5_aux:	Thr (ABCD) -> Thr_Aux (ABCD)
+bs_oaa6:	BM_OAA (ABCD) + FTHF (a) -> Met (ABCDa)
+bs_oaa6_aux:	Met (ABCDE) -> Met_Aux (ABCDE)
+bs_oaa7:	BM_OAA (ABCD) -> Asn (ABCD)
+bs_oaa7_aux:	Asn (ABCD) -> Asn_Aux (ABCD)
+out_co2:	CO2 (A) -> CO2_out (A)
+out_Ac:	AcCoA (AB) -> Acetate (AB)
+out_FTHF:	FTHF (A) -> FTHF_out (A)

tools/influx_data_manager/test-data/galaxy_test.opt

@@ -0,0 +1,4 @@
+# Created by 'ftbl2mtf e_coli.ftbl -o mtf/' at 2022-05-25 17:04:34 CEST +0200
+Id	Comment	Name	Value
+		commandArgs	--TIMEIT
+		posttreat_R	plot_smeas.R

tools/influx_data_manager/test-data/galaxy_test.tsv

@@ -0,0 +1,30 @@
+sample	metabolite	derivative	isotopologue	isotopic_inchi	area	corrected_area	isotopologue_fraction	residuum	mean_enrichment
+Sample_1	Fum__f0,1		0	InChI=1S/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H,5,6)(H,7,8)/p-2/b2-1+/a(C4+0)	376000	379808.0495	0.411686654	0	0.28976599
+Sample_1	Fum__f0,1		1	InChI=1S/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H,5,6)(H,7,8)/p-2/b2-1+/a(C1+1),(C3+0)	235000	236670.2676	0.256534822	0	0.28976599
+Sample_1	Fum__f3,4		2	InChI=1S/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H,5,6)(H,7,8)/p-2/b2-1+/a(C2+1),(C2+0)	127000	124721.3958	0.135189694	0	0.28976599
+Sample_1	Fum__f3,4		3	InChI=1S/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H,5,6)(H,7,8)/p-2/b2-1+/a(C3+1),(C1+0)	143000	142264.7934	0.15420557	-3.16E-17	0.28976599
+Sample_1	Fum__f3,4		4	InChI=1S/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H,5,6)(H,7,8)/p-2/b2-1+/a(C4+1)	40000	39101.34875	0.04238326	7.90E-18	0.28976599
+Sample_1	OA		0	/a(C4+0)	0	0			
+Sample_1	OA		1	/a(C1+1),(C3+0)	0	0			
+Sample_1	OA		2	/a(C2+1),(C2+0)	0	0			
+Sample_1	OA		3	/a(C3+1),(C1+0)	0	0			
+Sample_1	OA		4	/a(C4+1)	0	0
+Sample_1	aKG		0	/a(C5+0)	761000	770757.2823	0.597105938	-2.00E-07	0.152393093
+Sample_1	aKG		1	/a(C1+1),(C4+0)	95100	94408.21105	0.073138074	-1.12E-07	0.152393093
+Sample_1	aKG		2	/a(C2+1),(C3+0)	391000	387815.2021	0.300440574	3.24E-05	0.152393093
+Sample_1	aKG		3	/a(C3+1),(C2+0)	39300	37840.97105	0.029315414	1.10E-05	0.152393093
+Sample_1	aKG		4	/a(C4+1),(C1+0)	0	0	0	-0.003157789	0.152393093
+Sample_1	aKG		5	/a(C5+1)	0	0	0	-0.000308026	0.152393093
+Sample_1	G3P		0	/a(C3+0)	715000	720817.8432	0.503717946	-8.14E-17	0.230797296
+Sample_1	G3P		1	/a(C1+1),(C2+0)	557000	560128.1628	0.39142567	8.14E-17	0.230797296
+Sample_1	G3P		2	/a(C2+1),(C1+0)	24800	19465.7317	0.013602935	-5.09E-17	0.230797296
+Sample_1	G3P		3	/a(C3+1)	133000	130583.2255	0.091253449	1.22E-16	0.230797296
+Sample_1	2/3PG		0	/a(C3+0)	1430000	1441469.898	0.269515204	0	0.350613298
+Sample_1	2/3PG		1	/a(C1+1),(C2+0)	2920000	2940779.044	0.549844755	0	0.350613298
+Sample_1	2/3PG		2	/a(C2+1),(C1+0)	226000	213534.0151	0.039924985	1.09E-17	0.350613298
+Sample_1	2/3PG		3	/a(C3+1)	765000	752597.6843	0.140715057	0	0.350613298
+Sample_1	E4P		0	/a(C4+0)	854	863.1453281	0.041336917	2.43E-14	0.38172391
+Sample_1	E4P		1	/a(C1+1),(C3+0)	10200	10307.12055	0.493618598	-1.05E-14	0.38172391
+Sample_1	E4P		2	/a(C2+1),(C2+0)	7760	7810.814464	0.374067934	1.51E-14	0.38172391
+Sample_1	E4P		3	/a(C3+1),(C1+0)	1730	1644.671968	0.078765031	-2.33E-14	0.38172391
+Sample_1	E4P		4	/a(C4+1)	320	254.9855408	0.01221152	3.42E-14	0.38172391

tools/influx_data_manager/test-data/galaxy_test.tvar

@@ -0,0 +1,102 @@
+# Created by 'ftbl2mtf e_coli.ftbl -o mtf/' at 2022-05-25 17:04:34 CEST +0200
+Id	Comment	Name	Kind	Type	Value
+		Glucupt_1	NET	F	0.7
+		Glucupt_U	NET	D	
+		pgi	NET	D	
+		pfk	NET	D	
+		ald	NET	D	
+		pgk	NET	D	
+		eno	NET	D	
+		pyk	NET	F	1.4
+		zwf	NET	F	0.2
+		gnd	NET	F	0.15062
+		edd	NET	D	
+		ta	NET	D	
+		tk1	NET	D	
+		tk2	NET	D	
+		pdh	NET	D	
+		citsynth	NET	D	
+		idh	NET	D	
+		akgdh	NET	D	
+		fum_a	NET	D	
+		fum_b	NET	D	
+		maldh	NET	D	
+		ppc	NET	D	
+		mae	NET	D	
+		bs_glc6P	NET	C	0.0109
+		bs_fru6P	NET	C	0.0038
+		bs_pga	NET	C	0.0791
+		bs_pga_aux	NET	D	
+		bs_pga1	NET	D	
+		bs_pga1_aux	NET	C	0.0109
+		bs_pga2	NET	D	
+		bs_pga2_aux	NET	C	0.0046
+		bs_pga3	NET	D	
+		bs_pga3_aux	NET	C	0.0308
+		bs_DHAP	NET	C	0.0068
+		bs_pyr	NET	C	0.1501
+		bs_pyr1	NET	D	
+		bs_pyr1_aux	NET	D	
+		bs_pyr2	NET	D	
+		bs_pyr4	NET	D	
+		bs_pyr4_aux	NET	C	0.0213
+		bs_pyr3	NET	D	
+		bs_pyr3_aux	NET	C	0.0227
+		bs_e4p	NET	D	
+		bs_rib5p	NET	C	0.0476
+		bs_rib5p1	NET	D	
+		bs_rib5p1_aux	NET	C	0.0048
+		bs_rib5p2	NET	D	
+		bs_pep	NET	C	0.0381
+		bs_pep1	NET	D	
+		bs_pep2	NET	D	
+		bs_pep3a	NET	D	
+		bs_pep3b	NET	D	
+		bs_pep3_aux	NET	C	0.0093
+		bs_pep4a	NET	D	
+		bs_pep4b	NET	D	
+		bs_pep4_aux	NET	C	0.0069
+		bs_pep5	NET	C	0.0027
+		bs_pep6	NET	D	
+		bs_pep6_aux	NET	D	
+		bs_pep7	NET	D	
+		bs_accoa	NET	C	0.1565
+		bs_accoa_aux	NET	D	
+		bs_akg	NET	C	0.0571
+		bs_akg1	NET	D	
+		bs_akg2	NET	C	0.0111
+		bs_akg3	NET	C	0.0132
+		bs_akg4	NET	D	
+		bs_akg4_aux	NET	D	
+		bs_oaa	NET	C	0.0947
+		bs_oaa1	NET	D	
+		bs_oaa1_aux	NET	C	0.0121
+		bs_oaa2	NET	D	
+		bs_oaa2_aux	NET	C	0.0146
+		bs_oaa3a	NET	D	
+		bs_oaa3b	NET	D	
+		bs_oaa3_aux	NET	C	0.0173
+		bs_oaa4	NET	D	
+		bs_oaa5	NET	D	
+		bs_oaa5_aux	NET	C	0.0128
+		bs_oaa6	NET	D	
+		bs_oaa6_aux	NET	C	0.0077
+		bs_oaa7	NET	D	
+		bs_oaa7_aux	NET	C	0.0121
+		out_co2	NET	D	
+		out_Ac	NET	F	0.213
+		out_FTHF	NET	D	
+		pgi	XCH	C	0.752386
+		ald	XCH	F	0.413926
+		pgk	XCH	C	0.984718
+		eno	XCH	F	0.800962
+		pyk	XCH	C	0.0109591
+		ta	XCH	F	0.359468
+		tk1	XCH	F	0.166316
+		tk2	XCH	F	2.11559e-03
+		pdh	XCH	C	0.0322745
+		fum_a	XCH	F	0.395958
+		fum_b	XCH	D	
+		maldh	XCH	C	0.647115
+		ppc	XCH	F	0.256772
+		bs_pga3	XCH	C	0.011799