# HG changeset patch
# User computational-metabolomics
# Date 1643994826 0
# Node ID 96b07722120178490ef3b643297e040a29151377
# Parent  57c4e74210854ce5158b99e5cd110522033fa67c
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a"

diff -r 57c4e7421085 -r 96b077221201 sirius_csifingerid.py
--- a/sirius_csifingerid.py	Fri Feb 04 10:15:28 2022 +0000
+++ b/sirius_csifingerid.py	Fri Feb 04 17:13:46 2022 +0000
@@ -42,7 +42,7 @@
     exit()
 
 if args.temp_dir:
-    wd = os.path.join(args.temp_dir, 'temp')
+    wd = os.path.join(args.temp_dir, 'temp_'+str(uuid.uuid4()))
     os.mkdir(wd)
 
     if not os.path.exists(wd):
@@ -396,33 +396,27 @@
                         # If rank_filter is zero then skip
                         continue
 
-                    if ('ConfidenceScore' in line
-                        and 0 < float(confidence_filter)
-                        and float(line['ConfidenceScore']) <
-                            float(confidence_filter)):
-                        # filter out those annotations that are less than
-                        # the confidence filter value
-                        continue
+                    if 'ConfidenceScore' in line:
+                        if isinstance(line['ConfidenceScore'], str):
+                            # Value is NA or N/A
+                            continue
+
+                        if (0 < float(confidence_filter)
+                            and float(line['ConfidenceScore'])
+                                < float(confidence_filter)):
+                            # filter out those annotations that are less than
+                            # the confidence filter value
+                            continue
                     line.update(ad)
 
                     dwriter.writerow(line)
 
-    if backwards_compatible:
-        # Headers required in this format for tools that used
-        # v4.9.3 of SIRIUS-CSI:FingerID
-        s1 = "sed 's/InChIkey2D/inchikey2d/g' {r} > {r}".format(r=result_pth)
-        os.system(s1)
-        s2 = "sed 's/CSI:FingerIDScore/Score/' {r} > {r}".format(r=result_pth)
-        os.system(s2)
-
 
 concat_output('compound_identifications.tsv',
               args.annotations_result_pth,
               args.rank_filter,
-              args.confidence_filter,
-              args.backwards_compatible)
+              args.confidence_filter)
 concat_output('canopus_summary.tsv',
               args.canopus_result_pth,
               0,
-              0,
-              False)
+              0)
diff -r 57c4e7421085 -r 96b077221201 sirius_csifingerid.xml
--- a/sirius_csifingerid.xml	Fri Feb 04 10:15:28 2022 +0000
+++ b/sirius_csifingerid.xml	Fri Feb 04 17:13:46 2022 +0000
@@ -1,5 +1,5 @@
 <tool id="sirius_csifingerid" name="SIRIUS-CSI:FingerID"
-      version="4.9.8+galaxy1" profile="19.05">
+      version="4.9.8+galaxy2" profile="19.05">
     <description>is used to identify metabolites using single and
         tandem mass spectrometry</description>
     <requirements>
@@ -16,14 +16,14 @@
             --candidates $candidates
             --ppm_max $ppm_max
             --polarity $polarity
-            --out_dir .
+            --out_dir $__new_file_path__
             --canopus_result_pth canopus_all_summary.tsv
             --annotations_result_pth annotations_all_summary.tsv
             --cores_top_level 1
             --meta_select_col $meta_select_col
             --min_MSMS_peaks $min_MSMS_peaks
             --schema $schema
-            --temp_dir .
+            --temp_dir $__new_file_path__
 
             #if $adducts_cond.adducts_selector == 'select':
                 #for $a in $adducts_cond.adducts
@@ -51,9 +51,6 @@
 
             --confidence_filter $confidence_filter
 
-            #if $backwards_compatible
-                --backwards_compatible
-            #end if
 
     ]]></command>
     <inputs>
@@ -147,9 +144,6 @@
                label="Only show annotations greater than or or equal
                       to this value (default to show all annotations)"/>
 
-        <param argument="--backwards_compatible" type="boolean" checked="false"
-               label="Makes the outputs compatible with annotation workflows that used the old output from
-                      SIRIUS-CSI:FingerID v4.0.1"/>
     </inputs>
     <outputs>
         <data name="canopus_results" format="tsv" label="${tool.name} on ${on_string}: CANOPUS"
@@ -202,14 +196,6 @@
             <output name="canopus_results" file="canopus_RP022611_result_all_adducts.tsv"/>
         </test>
         <test>
-            <!-- Test for backward compa format-->
-            <param name="input" value="CCMSLIB00000578155.msp" ftype="msp"/>
-            <param name="profile" value="orbitrap"/>
-            <param name="backwards_compatible" value="--backwards_compatible"/>
-            <output name="annotation_results" file="bc_annotation_CCMSLIB00000578155_result.tsv"/>
-            <output name="canopus_results" file="bc_canopus_CCMSLIB00000578155_result.tsv"/>
-        </test>
-        <test>
             <!-- Test confidence filter  -->
             <param name="input" value="generic.msp" ftype="msp"/>
             <param name="confidence_filter" value="0.7"/>
diff -r 57c4e7421085 -r 96b077221201 test-data/bc_annotation_CCMSLIB00000578155_result.tsv
--- a/test-data/bc_annotation_CCMSLIB00000578155_result.tsv	Fri Feb 04 10:15:28 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-name	adduct	rank	formulaRank	#adducts	#predictedFPs	ConfidenceScore	CSI:FingerIDScore	ZodiacScore	SiriusScore	molecularFormula	adduct	InChIkey2D	InChI	name	smiles	xlogp	pubchemids	links	dbflags	ionMass	retentionTimeInSeconds	id
-D-GLUCOSE-6-PHOSPHATE	[M-H]-	1	1	1	1	0.2777991179997831	-40.17179067053119	N/A	17.8469785346642	C6H13O9P	[M-H]-	NBSCHQHZLSJFNQ	InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)	D-GLUCOSE-6-PHOSPHATE	C(C1C(C(C(C(O1)O)O)O)O)OP(=O)(O)O	-4.19999981	208;5958;65127;439198;439284;439404;439427;440100;447096;449526;4178491;4459709;9817215;9859975;10848963;12314997;11536233;10038266;12598269;11651816;11651817;11701643;10332946;10422797;10422798;11499884;16219407;21604864;21604865;23421197;23421199;23421200;25200774;25244236;24802166;42609823;44589902;44629605;46936284;51351673;51351674;59660207;59660208;66804219;72200063;71048769;70828590;90657928;90087729;92043642;89530481;89533633;92144442;92331698;92331699;92450038;102072969;101251820;100983220;124302956;124303605;129703999;129800866;133556303;134813555;135054589;135070792	HMDB:(1078 1401 3498);SuperNatural:(SN00005991 SN00006877 SN00368182 SN00005992);ZINC bio:(ZINC01529564 ZINC01532857 ZINC03869395 ZINC03869396 ZINC03869397 ZINC03869398 ZINC03875374 ZINC03875375 ZINC04096188 ZINC08551508 ZINC13540027);additional;MeSH:(65127 25244236);Plantcyc:(CPD-15711 GLC-6-P CPD-15712 CPD-1241 D-HEXOSE-6-PHOSPHATE MANNOSE-6P ALPHA-GLC-6-P);PubMed;NORMAN:(NS00015226);COCONUT:(CNP0093800 CNP0209092);KNApSAcK:(7307);Natural Products:(UNPD119019 UNPD208877);PubChem:(208 5958 65127 439198 439284 439404 439427 440100 447096 449526 4178491 4459709 9817215 9859975 10848963 12314997 11536233 10038266 12598269 11651816 11651817 11701643 10332946 10422797 10422798 11499884 16219407 21604864 21604865 23421197 23421199 23421200 25200774 25244236 24802166 42609823 44589902 44629605 46936284 51351673 51351674 59660207 59660208 66804219 72200063 71048769 70828590 90657928 90087729 92043642 89530481 89533633 92144442 92331698 92331699 92450038 102072969 101251820 100983220 124302956 124303605 129703999 129800866 133556303 134813555 135054589 135070792);CHEBI:(49728 91004 61548 58735 58247 134068 4170 4141 136602 58225 47944 43896 17719 48066 17665 61567 60332 61667 41076);PubChem class - bio and metabolites;KEGG:(C00275 C01172 C02965 C03735 C00668 C01113 C00092 C02962);YMDB:(2311 311 947 966 242);Training Set;Biocyc:(CPD-15711 GLC-6-P CPD-15712 CPD-1241 D-HEXOSE-6-PHOSPHATE MANNOSE-6P CPD1A0-6282 ALPHA-GLC-6-P SMA-0000014 SMA-0000409)	20965758	259.022	NaN	0_unknown_
diff -r 57c4e7421085 -r 96b077221201 test-data/bc_canopus_CCMSLIB00000578155_result.tsv
--- a/test-data/bc_canopus_CCMSLIB00000578155_result.tsv	Fri Feb 04 10:15:28 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-name	adduct	name	molecularFormula	adduct	most specific class	level 5	subclass	class	superclass	all classifications
-D-GLUCOSE-6-PHOSPHATE	[M-H]-	D-GLUCOSE-6-PHOSPHATE	C6H13O9P	[M-H]-	Hexose phosphates	Monosaccharides	Carbohydrates and carbohydrate conjugates	Organooxygen compounds	Organic oxygen compounds	Organic compounds; Organoheterocyclic compounds; Carbohydrates and carbohydrate conjugates; Alcohols and polyols; Ethers; Organic acids and derivatives; Organooxygen compounds; Organic phosphoric acids and derivatives; Phosphate esters; Hemiacetals; Hexoses; Monosaccharides; Monosaccharide phosphates; Secondary alcohols; Oxanes; Hexose phosphates; Polyols; Alkyl phosphates; Monoalkyl phosphates; Organic oxides; Oxacyclic compounds; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities