changeset 3:2ec9253a647e draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8714723083359049eb1a715a946851e07f8a3a20

--- a/ramclustr.xml	Wed Jun 29 10:00:10 2022 +0000
+++ b/ramclustr.xml	Tue Sep 20 14:43:56 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy1">
+<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy2">
     <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
     <macros>
         <import>macros.xml</import>
@@ -129,7 +129,7 @@
                     <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
                 </section>
             </section>
-            <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="10"/>
+            <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="20"/>
             <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
         </test>
         <test><!-- TEST 3 -->

--- a/ramclustr_wrapper.R	Wed Jun 29 10:00:10 2022 +0000
+++ b/ramclustr_wrapper.R	Tue Sep 20 14:43:56 2022 +0000
@@ -1,10 +1,9 @@
-store_output <- function(
-    ramclustr_obj,
-    output_merge_msp,
-    output_spec_abundance,
-    msp_file) {
+store_output <- function(ramclustr_obj,
+                         output_merge_msp,
+                         output_spec_abundance,
+                         msp_file) {
     RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp)
-    write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE)
+    write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE, quote = FALSE)
 
     if (!is.null(msp_file)) {
         exp_name <- ramclustr_obj$ExpDes[[1]][which(row.names(ramclustr_obj$ExpDes[[1]]) == "Experiment"), 1]
@@ -36,27 +35,25 @@
     return(data)
 }
 
-ramclustr_xcms <- function(
-    input_xcms,
-    use_pheno,
-    sr,
-    st = NULL,
-    cor_method,
-    maxt,
-    linkage,
-    min_module_size,
-    hmax,
-    deep_split,
-    normalize,
-    metadata_file = NULL,
-    qc_inj_range,
-    block_size,
-    mult,
-    mzdec,
-    rt_only_low_n,
-    replace_zeros,
-    exp_design = NULL
-) {
+ramclustr_xcms <- function(input_xcms,
+                           use_pheno,
+                           sr,
+                           st = NULL,
+                           cor_method,
+                           maxt,
+                           linkage,
+                           min_module_size,
+                           hmax,
+                           deep_split,
+                           normalize,
+                           metadata_file = NULL,
+                           qc_inj_range,
+                           block_size,
+                           mult,
+                           mzdec,
+                           rt_only_low_n,
+                           replace_zeros,
+                           exp_design = NULL) {
     obj <- load(input_xcms)
 
     batch <- NULL
@@ -100,33 +97,32 @@
         order = order,
         qc = qc,
         ExpDes = experiment
-        )
+    )
     return(x)
 }
 
-ramclustr_csv <- function(
-    ms,
-    idmsms,
-    sr,
-    st,
-    cor_method,
-    maxt,
-    linkage,
-    min_module_size,
-    hmax,
-    deep_split,
-    normalize,
-    metadata_file = NULL,
-    qc_inj_range,
-    block_size,
-    mult,
-    mzdec,
-    rt_only_low_n,
-    replace_zeros,
-    exp_design = NULL
-) {
-    if (!file.exists(idmsms))
+ramclustr_csv <- function(ms,
+                          idmsms,
+                          sr,
+                          st,
+                          cor_method,
+                          maxt,
+                          linkage,
+                          min_module_size,
+                          hmax,
+                          deep_split,
+                          normalize,
+                          metadata_file = NULL,
+                          qc_inj_range,
+                          block_size,
+                          mult,
+                          mzdec,
+                          rt_only_low_n,
+                          replace_zeros,
+                          exp_design = NULL) {
+    if (!file.exists(idmsms)) {
         idmsms <- NULL
+    }
 
     batch <- NULL
     order <- NULL
@@ -169,6 +165,6 @@
         order = order,
         qc = qc,
         ExpDes = experiment
-        )
-        return(x)
+    )
+    return(x)
 }

--- a/test-data/test1_spec_abundance_xcms_1.csv	Wed Jun 29 10:00:10 2022 +0000
+++ b/test-data/test1_spec_abundance_xcms_1.csv	Tue Sep 20 14:43:56 2022 +0000
@@ -1,21 +1,21 @@
-"","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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--- a/test-data/test2_spec_abundance_xcms_2.csv	Wed Jun 29 10:00:10 2022 +0000
+++ b/test-data/test2_spec_abundance_xcms_2.csv	Tue Sep 20 14:43:56 2022 +0000
@@ -1,6 +1,6 @@
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--- a/test-data/test3_spec_abundance_csv_1.csv	Wed Jun 29 10:00:10 2022 +0000
+++ b/test-data/test3_spec_abundance_csv_1.csv	Tue Sep 20 14:43:56 2022 +0000
@@ -1,4 +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
+,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