From 4fd563f194233b290ca5de5cf4938a2120287625 Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Mon, 25 Sep 2023 10:43:37 +0200
Subject: [PATCH 1/3] added tool

---
 tools/matchms/matchms_add_key.xml | 62 +++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 tools/matchms/matchms_add_key.xml

diff --git a/tools/matchms/matchms_add_key.xml b/tools/matchms/matchms_add_key.xml
new file mode 100644
index 00000000..4dc9e78e
--- /dev/null
+++ b/tools/matchms/matchms_add_key.xml
@@ -0,0 +1,62 @@
+<tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+    <description>Set metadata key in MSP to static value</description>
+    
+    <macros>
+        <import>macros.xml</import>
+        <import>help.xml</import>
+    </macros>
+
+    <expand macro="creator"/>
+
+    <edam_operations>
+        <edam_operation>operation_2409</edam_operation>
+    </edam_operations>
+    <expand macro="bio.tools"/>
+
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
+    </requirements>
+
+    <command detect_errors='aggressive'><![CDATA[
+        python ${matchms_python_cli}
+    ]]></command>
+
+<configfiles>
+<configfile name="matchms_python_cli">
+@init_logger@
+
+from matchms.importing import load_from_msp
+from matchms.exporting import save_as_msp
+spectra = list(load_from_msp("${spectral_library}", metadata_harmonization = "False"))
+new_spectra = []
+for spectrum in spectra:
+    spectrum.set("${key}", "${value}")
+    new_spectra.append(spectrum)
+save_as_msp(new_spectra, "${output}")
+</configfile>
+</configfiles>
+
+    <inputs>
+        <param label="Spectra file" name="spectral_library" type="data" format="msp"
+            help="Mass spectral library file to add key." />
+
+        <param label="Attribute Name" name="key" type="text" value="" help="Name of the attribute which will be assigned to all spectra records in the MSP." />
+        <param label="Value" name="value" type="text" value="" help="Value of the attribute which will be assigned to all spectra records in the MSP." />
+    </inputs>
+
+    <outputs>
+        <data label="${tool.name} on ${on_string}" name="output" format="msp">
+        </data>
+    </outputs>
+
+
+    <help><![CDATA[
+        Description
+        The tool take MSP file as an input and take as parameters the name of the 
+        attribute and its value which will be assigned to all spectra records in the MSP.
+    ]]></help>
+
+    <citations>
+        <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
+    </citations>
+</tool>

From a05ba5961b8832306e9e35ab46ebe6d83e04a12d Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Tue, 26 Sep 2023 12:32:57 +0200
Subject: [PATCH 2/3] added test and testdata

---
 tools/matchms/matchms_add_key.xml             |   8 +
 .../matchms/test-data/out_matchms_add_key.msp | 199 ++++++++++++++++++
 2 files changed, 207 insertions(+)
 create mode 100644 tools/matchms/test-data/out_matchms_add_key.msp

diff --git a/tools/matchms/matchms_add_key.xml b/tools/matchms/matchms_add_key.xml
index 4dc9e78e..a17de360 100644
--- a/tools/matchms/matchms_add_key.xml
+++ b/tools/matchms/matchms_add_key.xml
@@ -49,6 +49,14 @@ save_as_msp(new_spectra, "${output}")
         </data>
     </outputs>
 
+    <tests>
+        <test>
+            <param name="spectral_library" value="filtering/input.msp" ftype="msp"/>
+            <param name="key" value="tool_used"/>
+            <param name="value" value="matchms"/>
+            <output name="output" file="out_matchms_add_key.msp" ftype="msp"/>
+        </test>
+    </tests>
 
     <help><![CDATA[
         Description
diff --git a/tools/matchms/test-data/out_matchms_add_key.msp b/tools/matchms/test-data/out_matchms_add_key.msp
new file mode 100644
index 00000000..89d9650c
--- /dev/null
+++ b/tools/matchms/test-data/out_matchms_add_key.msp
@@ -0,0 +1,199 @@
+IONMODE: Negative
+SPECTRUMTYPE: Centroid
+COMPOUND_NAME: C001
+RETENTION_TIME: 38.74
+RETENTION_INDEX: -1
+TOOL_USED: matchms
+NUM PEAKS: 57
+138.9121    10186226.0
+148.9337    1008656.0
+175.0641    26780143.0
+186.1095    2675456.0
+196.8658    21390430.0
+198.8647    21688594.0
+200.8848    7742528.0
+206.9034    26130980.0
+216.9205    32607700.0
+234.0134    2550129.0
+254.8252    23747536.0
+256.8215    31377637.0
+258.8237    15532799.0
+266.8652    9805546.0
+268.8537    3090354.0
+306.9914    3169316.0
+312.7841    10051801.0
+316.7777    10734168.0
+322.8157    6317648.0
+324.9549    8619910.0
+334.849     4178412.0
+342.8093    3285552.0
+349.9455    2050695.0
+350.9875    6150799.0
+351.941     1965882.0
+366.8281    3253770.0
+370.7418    9765463.0
+372.7383    19374863.0
+382.8218    12815572.0
+384.8177    8311500.0
+392.7685    10913351.0
+413.2664    3965867.0
+426.7772    5431633.0
+428.7834    8554675.0
+434.7287    9943329.0
+436.8161    3705247.0
+440.7322    10603010.0
+442.7401    8271752.0
+450.7016    8762673.0
+460.7076    4528973.0
+462.7862    2123666.0
+484.7242    4273989.0
+486.7743    4886062.0
+488.6825    12267966.0
+492.744     7662344.0
+494.8953    7188793.0
+498.8794    6811405.0
+500.8484    6520691.0
+502.7832    3567833.0
+510.763     4989757.0
+518.7415    4243468.0
+546.6093    7177067.0
+550.6949    6104789.0
+566.5977    5171811.0
+612.6927    2005587.0
+676.6436    1982714.0
+800.4451    2792137.0
+
+IONMODE: Negative
+SPECTRUMTYPE: Centroid
+COMPOUND_NAME: C002
+RETENTION_TIME: 520.25
+RETENTION_INDEX: 1234.5
+TOOL_USED: matchms
+NUM PEAKS: 35
+131.1733    1971789.0
+267.2688    6103973.0
+279.0196    1946255.0
+289.6491    46498377.0
+301.1565    15185412.0
+309.1649    18045974.0
+310.1623    295359836.0
+311.1658    13124727.0
+312.0296    38757284.0
+330.6757    12666597.0
+525.375     1073323842.0
+526.3783    181668883.0
+527.3812    23642795.0
+551.3321    111616808.0
+552.3348    28340614.0
+553.3314    2609936.0
+562.3269    7538206.0
+578.2905    7578406.0
+619.3008    4742103.0
+624.296     11790213.0
+813.5403    25060147.0
+814.5336    5865975.0
+955.1171    2322927.0
+1047.7378   150394804.0
+1048.7399   90978863.0
+1049.7432   29946438.0
+1050.7453   6807767.0
+1069.7158   5074652.0
+1074.1979   3402288.0
+1075.1968   33352763.0
+1076.2004   10417953.0
+1101.6535   2023916.0
+1206.3127   3738816.0
+1216.8041   4439324.0
+1217.807    3565334.0
+
+IONMODE: Negative
+SPECTRUMTYPE: Centroid
+COMPOUND_NAME: C003
+RETENTION_TIME: 483.67
+TOOL_USED: matchms
+NUM PEAKS: 26
+265.2529    11366224.0
+266.2564    1420444.0
+279.6362    29849749.0
+280.6546    8848921.0
+288.6414    202172046.0
+378.2093    15309961.0
+379.1966    2902366.0
+522.3565    4089569222.0
+523.354     1201714423.0
+549.3267    63300808.0
+576.2749    7386007.0
+577.3074    2354251.0
+617.2778    2323470.0
+625.4543    4040374.0
+796.9808    13576738.0
+797.9841    6368973.0
+809.9883    12596682.0
+810.9916    6601055.0
+1043.7028   144351468.0
+1044.7068   83271854.0
+1045.706    27998321.0
+1046.7131   6505178.0
+1058.1594   20718345.0
+1059.1626   6608764.0
+1071.1639   15461047.0
+1072.1671   5096642.0
+
+IONMODE: Negative
+SPECTRUMTYPE: Centroid
+COMPOUND_NAME: C004
+RETENTION_TIME: 473.48
+TOOL_USED: matchms
+NUM PEAKS: 24
+124.1405    6517662.0
+170.2437    1237313.0
+275.6336    28001849.0
+296.147     190395687.0
+482.3247    145772322.0
+483.3283    36245876.0
+496.34      12577588056.0
+497.3442    3337125302.0
+498.3462    532285213.0
+499.3493    68176083.0
+770.964     49250157.0
+771.9675    22666873.0
+783.9721    9839299.0
+784.9749    3622908.0
+949.6233    8009033.0
+950.6274    3674694.0
+991.6726    1420557258.0
+992.6749    763118028.0
+993.6787    239161906.0
+994.6801    53549573.0
+1017.6897   168186952.0
+1018.6656   120599518.0
+1019.6555   57647644.0
+1020.6591   12469103.0
+
+IONMODE: Negative
+SPECTRUMTYPE: Centroid
+COMPOUND_NAME: C005
+RETENTION_TIME: 41.72
+TOOL_USED: matchms
+NUM PEAKS: 20
+218.1386    14009249.0
+337.0623    88672453.0
+338.0654    8770055.0
+353.0361    37061354.0
+359.0443    48435582.0
+360.0459    5025128.0
+375.018     29159485.0
+376.0216    2740193.0
+381.0261    13522755.0
+396.9999    10317665.0
+417.0027    13822994.0
+418.9966    4386311.0
+432.9764    9779399.0
+438.9851    11307111.0
+440.9796    3364168.0
+454.9592    9820452.0
+456.9603    3774845.0
+470.9263    3632486.0
+512.8989    4072570.0
+572.871     3485486.0
+

From 492ae0666737fa8c213d52a10840a4e9297cfa8f Mon Sep 17 00:00:00 2001
From: Helge Hecht <helge.hecht@recetox.muni.cz>
Date: Wed, 27 Sep 2023 12:37:11 +0000
Subject: [PATCH 3/3] Update tools/matchms/matchms_add_key.xml

---
 tools/matchms/matchms_add_key.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/matchms/matchms_add_key.xml b/tools/matchms/matchms_add_key.xml
index a17de360..33851be0 100644
--- a/tools/matchms/matchms_add_key.xml
+++ b/tools/matchms/matchms_add_key.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+<tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>Set metadata key in MSP to static value</description>
     
     <macros>