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Changeset 7:2a1f120a6874 (2023-01-10)

Previous changeset 6:77abacd33c31 (2022-09-30)

Commit message:
planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723

modified:
MS2snoop.R
MS2snoop.xml
README.md
macros.xml
test-data/smol/out-smol-base.tsv
test-data/smol/out-smol-delta-0.05mz.tsv
test-data/smol/out-smol-delta-8.542.tsv

diff -r 77abacd33c31 -r 2a1f120a6874 MS2snoop.R
--- a/MS2snoop.R Fri Sep 30 16:18:56 2022 +0000
+++ b/MS2snoop.R Tue Jan 10 11:07:48 2023 +0000

[

@@ -54,7 +54,8 @@
   mzref,
   spectra,
   processing_parameters,
-  background = !TRUE
+  background = !TRUE,
+  show_sirius_outputs = !TRUE
) {
   if (is.vector(mzref) && length(mzref) > 1) {
     return(lapply(
@@ -89,13 +90,16 @@
       "-i='%s'",
       "-o='%s'",
       "tree",
-      ## loglevel is not working taken into account during
-      ## sirius startup, so we filter outputs...
-      "2>&1 | grep '^(WARNING|SEVERE)'"
+      "2>&1"
     ),
     input,
     output
   )
+  if (!show_sirius_outputs) {
+    ## loglevel is not taken into account during
+    ## sirius startup, so we filter outputs...
+    command <- paste(command, "| grep '^(WARNING|SEVERE)'")
+  }
   verbose_catf(
     ">> Sirius is running %swith the command: %s\n",
     if (background) "in the background " else "",
@@ -189,7 +193,8 @@
     return(rep(NA, length(mz_list)))
   }
   if (!is.null(trees_filename)) {
-    sirius_results <- cbind(sirius_results, extract_sirius_ppm(trees_filename))
+    extracted_ppm <- extract_sirius_ppm(trees_filename)
+    sirius_results <- cbind(sirius_results, extracted_ppm)
   } else {
     return(rep(NA, length(mz_list)))
   }
@@ -210,7 +215,7 @@

   for (index in seq_len(nrow(sirius_results))) {
     result <- sirius_results[index, ]
-    filter <- which(order(abs(fragment_matchings$mz - result$mz)) == 1)
+    filter <- order(abs(fragment_matchings$mz - result$mz))[1]
     fragment_matchings[filter, "formula"] <- result$formula
     fragment_matchings[filter, "ppm"] <- result$ppm
     catf(
@@ -1124,7 +1129,7 @@

zip_pdfs <- function(processing_parameters) {
   if (processing_parameters$do_pdf) {
-    if (zip <- Sys.getenv("R_ZIPCMD", "zip") == "") {
+    if ((zip <- Sys.getenv("R_ZIPCMD", "zip")) == "") {
       catf("R could not fin the zip executable. Trying luck: zip = \"zip\"")
       zip <- "zip"
     } else {

diff -r 77abacd33c31 -r 2a1f120a6874 MS2snoop.xml
--- a/MS2snoop.xml Fri Sep 30 16:18:56 2022 +0000
+++ b/MS2snoop.xml Tue Jan 10 11:07:48 2023 +0000

[

@@ -48,9 +48,15 @@
     --ionization '$sirius.ionization'
     --fragment_match_delta '$sirius.fragment_match_delta'
     --fragment_match_delta_unit '$sirius.fragment_match_delta_unit'
-    $advenced.pdf
+    #if $advenced.pdf:
+        --pdf_path './out.zip'
+    #end if
     $advenced.debug
     $advenced.verbose
+#if $advenced.pdf:
+&& cat ./out.zip > '$pdf_output'
+#end if
+
]]>
     </command>
     <inputs>
@@ -128,7 +134,7 @@
         </section>

         <section title="Advenced Options" name="advenced">
-            <param argument="--pdf" type="boolean" truevalue="--pdf_path '$pdf_output'" falsevalue="" value="" optional="true"
+            <param argument="--pdf" type="boolean" value="" optional="true"
                 label="Output PDF"
                 help="The tool will output some pdf in a zip file"
             />
@@ -143,14 +149,14 @@
         </section>
     </inputs>
     <outputs>
-        <data name="frag_result_txt" format="tsv" label="${tool.name} on ${peaklist_frag_tsv.name}" />
-        <data name="pdf_output" format="zip" label="${tool.name} PDFs for ${peaklist_frag_tsv.name}">
+        <data name="frag_result_txt" format="tsv" label="${tool.name}_on_${peaklist_frag_tsv.name}" />
+        <data name="pdf_output" format="zip" label="${tool.name}_PDFs_for_${peaklist_frag_tsv.name}">
             <filter>advenced['pdf']</filter>
         </data>
     </outputs>
     <tests>
         <test>
-            
+            
             <param name="compound_txt" value="compounds_pos.txt" />
             <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
             <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
@@ -163,7 +169,7 @@
         </test>

         <test>
-            
+            
             <param name="compound_txt" value="compounds_pos.txt" />
             <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
             <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
@@ -177,7 +183,7 @@
         </test>

         <test>
-            
+            
             <param name="compound_txt" value="compounds_pos.txt" />
             <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
             <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
@@ -191,7 +197,7 @@
         </test>

         <test>
-            
+            
             <param name="compound_txt" value="compounds_pos.txt" />
             <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
             <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
@@ -207,7 +213,7 @@

         <test>
             
             <param name="compound_txt" value="compounds_pos.csv" />
@@ -224,7 +230,7 @@

         <test>
             
             <param name="ionization" value="[M+?]+" />
@@ -237,7 +243,7 @@

         <test>
             
             <param name="pdf" value="True" />
             <param name="ionization" value="[M+?]+" />
@@ -250,7 +256,7 @@

         <test>
             
             <param name="ionization" value="[M+?]+" />
             <param name="mzdecimal" value="3" />
@@ -263,7 +269,7 @@

         <test>
             
             <param name="ionization" value="[M+?]+" />
             <param name="mzdecimal" value="3" />
@@ -278,7 +284,7 @@
         
         <test expect_exit_code="2" expect_failure="true">
             
             <param name="compound_txt" value="compounds_pos_old_format.txt" />

diff -r 77abacd33c31 -r 2a1f120a6874 README.md
--- a/README.md Fri Sep 30 16:18:56 2022 +0000
+++ b/README.md Tue Jan 10 11:07:48 2023 +0000

@@ -5,7 +5,7 @@
-----------

  * **@name**: MS2 Snoop
- * **@version**: 2.2.0
+ * **@version**: 2.2.1
  * **@authors**: Jean François Martin (INRAE), Kevin Wagner (INRAE)
  * **@maintainers**: Lain Pavot (PFEM - INRAE - MetaboHUB)
  * **@init date**: 2022, April

diff -r 77abacd33c31 -r 2a1f120a6874 macros.xml
--- a/macros.xml Fri Sep 30 16:18:56 2022 +0000
+++ b/macros.xml Tue Jan 10 11:07:48 2023 +0000

@@ -138,7 +138,7 @@
]]>
     </token>

-    <token name="@TOOL_VERSION@">2.2.0</token>
+    <token name="@TOOL_VERSION@">2.2.1</token>
     <token name="@VERSION_SUFFIX@">0</token>

     <xml name="has_smol_stdout">

diff -r 77abacd33c31 -r 2a1f120a6874 test-data/smol/out-smol-base.tsv
--- a/test-data/smol/out-smol-base.tsv Fri Sep 30 16:18:56 2022 +0000
+++ b/test-data/smol/out-smol-base.tsv Tue Jan 10 11:07:48 2023 +0000

@@ -1,18 +1,18 @@
"compoundName" "inchikey" "elemcomposition" "fragment" "fragment_mz" "ppm" "fileid" "CorWithPrecursor" "AbsoluteIntensity" "relativeIntensity" "corValid"
"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C13H8O4" 229.05 2.02930325023702 "1" NA 203723.75 0.932156767504374 NA
"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA 312.059 NA "1" NA 3981.51538085938 0.0182177900573243 NA
-"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA 313.068 NA "1" NA 7264.93603515625 0.0332413834452649 NA
-"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C17H12O6" 367.081 -8.51110969664126 "1" NA 218550.953125 1 NA
-"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C20H14O7" 451.115 -0.624494567969591 "1" NA 135964.078125 0.622116152690652 NA
+"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C17H12O6" 313.068 -8.51110969664126 "1" NA 7264.93603515625 0.0332413834452649 NA
+"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C20H14O7" 367.081 -0.624494567969591 "1" NA 218550.953125 1 NA
+"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA 451.115 NA "1" NA 135964.078125 0.622116152690652 NA
"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA 109.101 NA "1" NA 1663.78308105469 1 NA
"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA 140.951 NA "1" NA 1119.27758789062 0.672730478291135 NA
"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA 55.575 NA "1" NA 959.281677246094 0.00801122428782145 NA
-"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA 278.081 NA "1" NA 49810.07421875 0.415977585963074 NA
-"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" "C17H11NO3" 323.106 -0.610124713635454 "1" 1 119742.20703125 1 TRUE
+"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" "C17H11NO3" 278.081 -0.610124713635454 "1" NA 49810.07421875 0.415977585963074 NA
+"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA 323.106 NA "1" 1 119742.20703125 1 TRUE
"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 51.94 NA "1" NA 1706.40014648438 0.0178528316194543 NA
"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C5H6" 67.054 -3.38002342189334 "1" NA 1413.32275390625 0.0147865746503924 NA
-"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 122.059 NA "1" NA 40171.04296875 0.420280593374599 NA
-"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C7H7NO" 135.117 -8.52289540743972 "1" NA 95581.484375 1 NA
+"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C7H7NO" 122.059 -8.52289540743972 "1" NA 40171.04296875 0.420280593374599 NA
+"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 135.117 NA "1" NA 95581.484375 1 NA
"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 232.845 NA "1" NA 17855.763671875 0.186811952007572 NA
"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 135.071 NA "1" NA 1388.24841308594 0.0111932237930481 NA
"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 177.092 NA "1" NA 1346.46130371094 0.0108563010474573 NA

diff -r 77abacd33c31 -r 2a1f120a6874 test-data/smol/out-smol-delta-0.05mz.tsv
--- a/test-data/smol/out-smol-delta-0.05mz.tsv Fri Sep 30 16:18:56 2022 +0000
+++ b/test-data/smol/out-smol-delta-0.05mz.tsv Tue Jan 10 11:07:48 2023 +0000

diff -r 77abacd33c31 -r 2a1f120a6874 test-data/smol/out-smol-delta-8.542.tsv
--- a/test-data/smol/out-smol-delta-8.542.tsv Fri Sep 30 16:18:56 2022 +0000
+++ b/test-data/smol/out-smol-delta-8.542.tsv Tue Jan 10 11:07:48 2023 +0000