# HG changeset patch
# User recetox
# Date 1713267005 0
# Node ID c043e1fd79d136a2772ba1d6d490af23641c91c5
# Parent  09cabbc3d12db6f15f1f7cef6daa2b9093b57c3a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4b8a43b863ff8a0ff1d5a08e516068853adf358d

diff -r 09cabbc3d12d -r c043e1fd79d1 ramclustr.xml
--- a/ramclustr.xml	Thu Oct 12 13:30:54 2023 +0000
+++ b/ramclustr.xml	Tue Apr 16 11:30:05 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy3" profile="21.09">
+<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy4" profile="21.09">
     <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
     <macros>
         <import>macros.xml</import>
@@ -153,7 +153,7 @@
     </inputs>
 
     <outputs>
-        <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
+        <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="tsv" />
         <expand macro="output_msp"/>
     </outputs>
 
@@ -175,7 +175,7 @@
                 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
             </section>
             <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>
-            <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
+            <output name="spec_abundance" file="test1_spec_abundance_xcms_1.tsv" ftype="tsv" compare="sim_size" delta="100"/>
         </test>
         <test expect_num_outputs="2"><!-- TEST 2 -->
             <section name="filetype">
@@ -196,7 +196,7 @@
                 </section>
             </section>
             <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="100"/>
-            <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
+            <output name="spec_abundance" file="test2_spec_abundance_xcms_2.tsv" ftype="tsv" compare="sim_size" delta="100"/>
         </test>
         <test expect_num_outputs="2"><!-- TEST 3 -->
             <section name="filetype">
@@ -214,7 +214,7 @@
                 <param name="mult" value="1"/>
             </section>
             <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/>
-            <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/>
+            <output name="spec_abundance" file="test3_spec_abundance_csv_1.tsv" ftype="tsv"/>
         </test>
         <test expect_num_outputs="2"><!-- TEST 4 -->
             <section name="filetype">
diff -r 09cabbc3d12d -r c043e1fd79d1 ramclustr_wrapper.R
--- a/ramclustr_wrapper.R	Thu Oct 12 13:30:54 2023 +0000
+++ b/ramclustr_wrapper.R	Tue Apr 16 11:30:05 2024 +0000
@@ -3,9 +3,9 @@
                          output_spec_abundance,
                          msp_file) {
   RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp)
-  write.csv(ramclustr_obj$SpecAbund,
+  write.table(ramclustr_obj$SpecAbund,
     file = output_spec_abundance,
-    row.names = TRUE, quote = FALSE
+    row.names = TRUE, quote = FALSE, col.names = NA, sep = "\t"
   )
 
   if (!is.null(msp_file)) {
diff -r 09cabbc3d12d -r c043e1fd79d1 test-data/test1_spec_abundance_xcms_1.csv
--- a/test-data/test1_spec_abundance_xcms_1.csv	Thu Oct 12 13:30:54 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-,C001,C002,C003,C004,C005,C006,C007,C008,C009,C010,C011,C012,C013,C014,C015,C016,C017,C018,C019,C020,C021,C022,C023,C024,C025,C026,C027,C028,C029,C030,C031,C032,C033,C034,C035,C036,C037,C038,C039,C040,C041,C042,C043,C044,C045,C046,C047,C048,C049,C050,C051,C052,C053,C054,C055,C056,C057,C058,C059,C060,C061,C062,C063,C064,C065,C066,C067,C068,C069,C070,C071,C072,C073,C074,C075,C076,C077,C078,C079,C080,C081,C082,C083,C084,C085,C086,C087,C088,C089,C090,C091,C092,C093,C094,C095,C096,C097,C098,C099,C100,C101,C102,C103,C104,C105,C106,C107,C108,C109,C110,C111,C112,C113,C114,C115,C116,C117,C118,C119,C120,C121,C122,C123,C124,C125,C126,C127,C128,C129,C130,C131,C132,C133,C134,C135,C136,C137,C138,C139,C140,C141,C142,C143,C144,C145,C146,C147,C148,C149,C150,C151,C152,C153,C154,C155,C156,C157,C158,C159,C160,C161,C162,C163,C164,C165,C166,C167,C168,C169,C170,C171,C172,C173,C174
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diff -r 09cabbc3d12d -r c043e1fd79d1 test-data/test1_spec_abundance_xcms_1.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1_spec_abundance_xcms_1.tsv	Tue Apr 16 11:30:05 2024 +0000
@@ -0,0 +1,21 @@
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diff -r 09cabbc3d12d -r c043e1fd79d1 test-data/test2_spec_abundance_xcms_2.csv
--- a/test-data/test2_spec_abundance_xcms_2.csv	Thu Oct 12 13:30:54 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
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diff -r 09cabbc3d12d -r c043e1fd79d1 test-data/test2_spec_abundance_xcms_2.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2_spec_abundance_xcms_2.tsv	Tue Apr 16 11:30:05 2024 +0000
@@ -0,0 +1,6 @@
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diff -r 09cabbc3d12d -r c043e1fd79d1 test-data/test3_spec_abundance_csv_1.csv
--- a/test-data/test3_spec_abundance_csv_1.csv	Thu Oct 12 13:30:54 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-,C01,C02,C03,C04,C05,C06,C07,C08,C09,C10,C11,C12,C13,C14,C15,C16,C17,C18,C19,C20,C21,C22
-dataset_10908,1143359.6024874,14232152.476587,50449.9418344623,705676.707142857,37132.3539979397,29822.3430533531,48305.5183116056,16320.5463588464,233029.800680246,47298.0528173405,34827.0153828901,24530.3375165206,64864.9659048501,92746.0557178936,398852.491270866,20462.4444316982,315657.07173388,18224.8801651832,119901.384914687,112084.028638642,461198.718995128,10125.6569474277
-dataset_10909,1143359.6024874,14232152.476587,50449.9418344623,705676.707142857,37132.3539979397,29822.3430533531,48305.5183116056,16320.5463588464,233029.800680246,47298.0528173405,34827.0153828901,24530.3375165206,64864.9659048501,92746.0557178936,398852.491270866,20462.4444316982,315657.07173388,18224.8801651832,119901.384914687,112084.028638642,461198.718995128,10125.6569474277
-dataset_10910,1143359.6024874,14232152.476587,50449.9418344623,705676.707142857,37132.3539979397,29822.3430533531,48305.5183116056,16320.5463588464,233029.800680246,47298.0528173405,34827.0153828901,24530.3375165206,64864.9659048501,92746.0557178936,398852.491270866,20462.4444316982,315657.07173388,18224.8801651832,119901.384914687,112084.028638642,461198.718995128,10125.6569474277
diff -r 09cabbc3d12d -r c043e1fd79d1 test-data/test3_spec_abundance_csv_1.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test3_spec_abundance_csv_1.tsv	Tue Apr 16 11:30:05 2024 +0000
@@ -0,0 +1,4 @@
+	C01	C02	C03	C04	C05	C06	C07	C08	C09	C10	C11	C12	C13	C14	C15	C16	C17	C18	C19	C20	C21	C22
+dataset_10908	1143359.6024874	14232152.476587	50449.9418344623	705676.707142857	37132.3539979397	29822.3430533531	48305.5183116056	16320.5463588464	233029.800680246	47298.0528173405	34827.0153828901	24530.3375165206	64864.9659048501	92746.0557178936	398852.491270866	20462.4444316982	315657.07173388	18224.8801651832	119901.384914687	112084.028638642	461198.718995128	10125.6569474277
+dataset_10909	1143359.6024874	14232152.476587	50449.9418344623	705676.707142857	37132.3539979397	29822.3430533531	48305.5183116056	16320.5463588464	233029.800680246	47298.0528173405	34827.0153828901	24530.3375165206	64864.9659048501	92746.0557178936	398852.491270866	20462.4444316982	315657.07173388	18224.8801651832	119901.384914687	112084.028638642	461198.718995128	10125.6569474277
+dataset_10910	1143359.6024874	14232152.476587	50449.9418344623	705676.707142857	37132.3539979397	29822.3430533531	48305.5183116056	16320.5463588464	233029.800680246	47298.0528173405	34827.0153828901	24530.3375165206	64864.9659048501	92746.0557178936	398852.491270866	20462.4444316982	315657.07173388	18224.8801651832	119901.384914687	112084.028638642	461198.718995128	10125.6569474277
diff -r 09cabbc3d12d -r c043e1fd79d1 test-data/test4_spec_abundance_csv_2.csv
--- a/test-data/test4_spec_abundance_csv_2.csv	Thu Oct 12 13:30:54 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-"","C01","C02","C03","C04","C05","C06","C07","C08","C09","C10","C11","C12","C13","C14","C15","C16","C17","C18","C19","C20","C21","C22","C23","C24","C25","C26","C27","C28","C29","C30","C31","C32","C33","C34","C35","C36","C37","C38"
-"dataset_10908",15486747.5366514,705676.707142857,29822.3430533531,224421.528087479,240472.056093119,83802.7176826829,53891.3450571771,46940.0774103402,22283.2365363616,398852.491270866,16487.928248967,1983470.1118411,11998.5253787137,55783.8355817233,185478.847522515,315657.07173388,39349.4112699936,21728.8824232737,32441.4747147792,119901.384914687,461198.718995128,19834.4473795901,43602.3586534436,31889.6464337142,68360.3997127846,21854.49991187,1073398.26666055,156861.055191184,493341.849474475,16176.4044227296,10125.6569474277,37890.4782477985,29454.7192721113,66717.3172710142,4822.46628554095,24485.0599767888,21288.8896720112,103775.906887161
-"dataset_10909",15486747.5366514,705676.707142857,29822.3430533531,224421.528087479,240472.056093119,83802.7176826829,53891.3450571771,46940.0774103402,22283.2365363616,398852.491270866,16487.928248967,1983470.1118411,11998.5253787137,55783.8355817233,185478.847522515,315657.07173388,39349.4112699936,21728.8824232737,32441.4747147792,119901.384914687,461198.718995128,19834.4473795901,43602.3586534436,31889.6464337142,68360.3997127846,21854.49991187,1073398.26666055,156861.055191184,493341.849474475,16176.4044227296,10125.6569474277,37890.4782477985,29454.7192721113,66717.3172710142,4822.46628554095,24485.0599767888,21288.8896720112,103775.906887161
-"dataset_10910",15486747.5366514,705676.707142857,29822.3430533531,224421.528087479,240472.056093119,83802.7176826829,53891.3450571771,46940.0774103402,22283.2365363616,398852.491270866,16487.928248967,1983470.1118411,11998.5253787137,55783.8355817233,185478.847522515,315657.07173388,39349.4112699936,21728.8824232737,32441.4747147792,119901.384914687,461198.718995128,19834.4473795901,43602.3586534436,31889.6464337142,68360.3997127846,21854.49991187,1073398.26666055,156861.055191184,493341.849474475,16176.4044227296,10125.6569474277,37890.4782477985,29454.7192721113,66717.3172710142,4822.46628554095,24485.0599767888,21288.8896720112,103775.906887161
diff -r 09cabbc3d12d -r c043e1fd79d1 test-data/test4_spec_abundance_csv_2.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test4_spec_abundance_csv_2.tsv	Tue Apr 16 11:30:05 2024 +0000
@@ -0,0 +1,4 @@
+""	"C01"	"C02"	"C03"	"C04"	"C05"	"C06"	"C07"	"C08"	"C09"	"C10"	"C11"	"C12"	"C13"	"C14"	"C15"	"C16"	"C17"	"C18"	"C19"	"C20"	"C21"	"C22"	"C23"	"C24"	"C25"	"C26"	"C27"	"C28"	"C29"	"C30"	"C31"	"C32"	"C33"	"C34"	"C35"	"C36"	"C37"	"C38"
+"dataset_10908"	15486747.5366514	705676.707142857	29822.3430533531	224421.528087479	240472.056093119	83802.7176826829	53891.3450571771	46940.0774103402	22283.2365363616	398852.491270866	16487.928248967	1983470.1118411	11998.5253787137	55783.8355817233	185478.847522515	315657.07173388	39349.4112699936	21728.8824232737	32441.4747147792	119901.384914687	461198.718995128	19834.4473795901	43602.3586534436	31889.6464337142	68360.3997127846	21854.49991187	1073398.26666055	156861.055191184	493341.849474475	16176.4044227296	10125.6569474277	37890.4782477985	29454.7192721113	66717.3172710142	4822.46628554095	24485.0599767888	21288.8896720112	103775.906887161
+"dataset_10909"	15486747.5366514	705676.707142857	29822.3430533531	224421.528087479	240472.056093119	83802.7176826829	53891.3450571771	46940.0774103402	22283.2365363616	398852.491270866	16487.928248967	1983470.1118411	11998.5253787137	55783.8355817233	185478.847522515	315657.07173388	39349.4112699936	21728.8824232737	32441.4747147792	119901.384914687	461198.718995128	19834.4473795901	43602.3586534436	31889.6464337142	68360.3997127846	21854.49991187	1073398.26666055	156861.055191184	493341.849474475	16176.4044227296	10125.6569474277	37890.4782477985	29454.7192721113	66717.3172710142	4822.46628554095	24485.0599767888	21288.8896720112	103775.906887161
+"dataset_10910"	15486747.5366514	705676.707142857	29822.3430533531	224421.528087479	240472.056093119	83802.7176826829	53891.3450571771	46940.0774103402	22283.2365363616	398852.491270866	16487.928248967	1983470.1118411	11998.5253787137	55783.8355817233	185478.847522515	315657.07173388	39349.4112699936	21728.8824232737	32441.4747147792	119901.384914687	461198.718995128	19834.4473795901	43602.3586534436	31889.6464337142	68360.3997127846	21854.49991187	1073398.26666055	156861.055191184	493341.849474475	16176.4044227296	10125.6569474277	37890.4782477985	29454.7192721113	66717.3172710142	4822.46628554095	24485.0599767888	21288.8896720112	103775.906887161
diff -r 09cabbc3d12d -r c043e1fd79d1 test-data/test5_spec_abundance.csv
--- a/test-data/test5_spec_abundance.csv	Thu Oct 12 13:30:54 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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diff -r 09cabbc3d12d -r c043e1fd79d1 test-data/test5_spec_abundance.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test5_spec_abundance.tsv	Tue Apr 16 11:30:05 2024 +0000
@@ -0,0 +1,10 @@
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