pulsarify all tools in the repo

tools/camera/abims_CAMERA_annotateDiffreport.xml

@@ -7,10 +7,14 @@
     </macros>
 
     <expand macro="requirements"/>
+    <required_files>
+        <include path="CAMERA_annotateDiffreport.r" />
+        <include path="lib.r" />
+    </required_files>
     <expand macro="stdio"/>
 
     <command><![CDATA[
-        @COMMAND_RSCRIPT@/CAMERA_annotateDiffreport.r
+        @COMMAND_RSCRIPT@CAMERA_annotateDiffreport.r
         image '$image'
 
         nSlaves \${GALAXY_SLOTS:-1}

tools/camera/abims_CAMERA_combinexsAnnos.xml

@@ -7,10 +7,14 @@
     </macros>
 
     <expand macro="requirements"/>
+    <required_files>
+        <include path="CAMERA_combinexsAnnos.r" />
+        <include path="lib.r" />
+    </required_files>
     <expand macro="stdio"/>
 
     <command><![CDATA[
-        @COMMAND_RSCRIPT@/CAMERA_combinexsAnnos.r
+        @COMMAND_RSCRIPT@CAMERA_combinexsAnnos.r
         image_pos '$image_pos'
         image_neg '$image_neg'
 

tools/camera/macros.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.48.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="0.4_3">r-snow</requirement>

tools/correlation_analysis/abims_correlation_analysis.xml

@@ -1,4 +1,4 @@
-<tool id="correlation_analysis" name="Metabolites Correlation Analysis" version="1.0.1+galaxy0" >
+<tool id="correlation_analysis" name="Metabolites Correlation Analysis" version="1.0.1+galaxy1" >
 
     <description>to highlight ion correlations considering PC-groups</description>
 
@@ -7,6 +7,9 @@
         <requirement type="package" version="0.8.8">r-reshape</requirement>
         <requirement type="package" version="7.3_53">r-mass</requirement>
     </requirements>
+    <required_files>
+        <include path="correlation_analysis.r" />
+    </required_files>
 
     <command detect_errors='exit_code'>
         Rscript '$__tool_directory__/correlation_analysis.r'

tools/ipo/ipo4retgroup.xml

@@ -1,4 +1,4 @@
-<tool id="ipo4retgroup" name="IPO for group and retcor" version="@TOOL_VERSION@+galaxy0">
+<tool id="ipo4retgroup" name="IPO for group and retcor" version="@TOOL_VERSION@+galaxy1">
 
     <description>IPO optimization process for xcms.groupChromPeaks and xcms.adjustRtime</description>
 
@@ -7,7 +7,10 @@
     </macros>
 
     <expand macro="requirements"/>
-
+    <required_files>
+        <include path="ipo4retgroup.r" />
+        <include path="lib.r" />
+    </required_files>
     <command detect_errors="exit_code"><![CDATA[
         LANG=C Rscript '$__tool_directory__/ipo4retgroup.r'
 

tools/ipo/ipo4xcmsSet.xml

@@ -1,4 +1,4 @@
-<tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="@TOOL_VERSION@+galaxy1">
+<tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="@TOOL_VERSION@+galaxy2">
 
     <description>IPO optimization process for xcms.findChromPeaks</description>
 
@@ -7,6 +7,10 @@
     </macros>
 
     <expand macro="requirements"/>
+    <required_files>
+        <include path="ipo4xcmsSet.r" />
+        <include path="lib.r" />
+    </required_files>
 
     <command detect_errors="exit_code"><![CDATA[
         LANG=C Rscript '$__tool_directory__/ipo4xcmsSet.r'

tools/kmd_hmdb_data_plot/kmd_hmdb_data_plot.xml

@@ -5,7 +5,7 @@
     <macros>
         <import>macro.xml</import>
         <token name="@TOOL_VERSION@">1.0.0</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <edam_topics>
         <edam_topic>topic_0091</edam_topic>
@@ -14,11 +14,16 @@
         <edam_operation>operation_3803</edam_operation>
     </edam_operations>
     <requirements>
+        <requirement type="package" version="8.1.4">click</requirement>
         <requirement type="package" version="3.10">python</requirement>
         <requirement type="package" version="2.0.3">pandas</requirement>
         <requirement type="package" version="5.15.0">plotly</requirement>
         <requirement type="package" version="1.0.1">kmd_hmdb_api_client</requirement>
     </requirements>
+    <required_files>
+        <include path="kmd_hmdb_interrogator.py" />
+        <include path="kmd_hmdb_plot_generator.py" />
+    </required_files>
     <command detect_errors="exit_code">
 <![CDATA[
 #if "get_data" in str($what.to_do)

tools/mixmodel4repeated_measures/mixmodel.xml

@@ -1,4 +1,4 @@
-<tool id="mixmodel4repeated_measures" name="mixmodel" version="3.1.0" profile="19.01">
+<tool id="mixmodel4repeated_measures" name="mixmodel" version="3.1.0+galaxy1" profile="19.01">
     <description>ANOVA for repeated measures statistics</description>
 
     <requirements>
@@ -8,6 +8,11 @@
         <requirement type="package" version="2.3">r-gridExtra</requirement>
         <requirement type="package" version="2.40.0">bioconductor-multtest</requirement>
     </requirements>
+    <required_files>
+        <include path="mixmodel_wrapper.R" />
+        <include path="mixmodel_script.R" />
+        <include path="diagmfl.R" />
+    </required_files>
 
     <command detect_errors="exit_code"><![CDATA[
         Rscript '$__tool_directory__/mixmodel_wrapper.R'
@@ -114,7 +119,7 @@
 
 .. class:: infomark
 
-**Authors** Natacha Lenuzza and Jean-Francois Martin wrote this wrapper of R repeated measure anova statistical tests. 
+**Authors** Natacha Lenuzza and Jean-Francois Martin wrote this wrapper of R repeated measure anova statistical tests.
 **Maintainers** Melanie Petera and Marie Tremblay-Franco (INRAE-MetaboHUB)
 
 MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (https://www.metabohub.fr/home.html)
@@ -188,7 +193,7 @@ Subject
 |
 
 Degrees of freedom
-| Method to use for degrees of freedom computation 
+| Method to use for degrees of freedom computation
 |
 
 Method for multiple testing correction
@@ -218,13 +223,13 @@ variableMetadata_out.tabular
 
 mixedmodel_Estimates
 | A pdf file is created with a graphical representation of differences among levels of factors with a color code for significance and an error bar.
-| Plots are only provided for features with at least one significant factor. 
+| Plots are only provided for features with at least one significant factor.
 
 
 mixedmodel_diagResiduals
 | if Perform diagnostic of the residuals" is set to yes(default) a pdf file is created with a a serie of
 | graphics outputed in order to assess the distribution of residuals to check the adjustment.
-| Plots are only provided for features with at least one factor being significant based on the non-corrected p-values. 
+| Plots are only provided for features with at least one factor being significant based on the non-corrected p-values.
 
 information.txt
 | File with all messages and warnings generated during the computation

tools/ms2snoop/MS2snoop.xml

@@ -19,6 +19,9 @@
         <requirement type="package" version="4.9.15">sirius-csifingerid</requirement>
         <requirement type="package" version="3.0">zip</requirement>
     </requirements>
+    <required_files>
+        <include type="literal" path="MS2snoop.R"/>
+    </required_files>
     <stdio>
         <exit_code range="1" level="fatal" description="Missing parameter error" />
         <exit_code range="2" level="fatal" description="Bad parameter's value" />
@@ -310,7 +313,7 @@ Description
 
 MS2snoop use results of msPurity to find spectra of standards listed in
 a compounds file. Check the fragments and precursor using correlation of
-among the different scans of fragments 
+among the different scans of fragments
 
 -----------------
 Workflow position

tools/ms2snoop/macros.xml

@@ -26,13 +26,13 @@ msPurity.frag4feature
 Compounds file
   | A tabulated, comma or semicolon separated values file whith
     compounds. Its format is as follow:
-  |  
+  |
   | At least 4 columns:
   | **compound_name**: The name of the compound
   | **mz**: The m/z ratio
   | **rtsec**: The retention time in seconds
   | **inchikey**: The compound's inchi key
-  |  
+  |
   | An optional column can be added:
   | **elemcomposition**: The elemental composition of the molecule
 
@@ -66,10 +66,10 @@ compound_fragments_result.tsv
   | tabular output
   | Array with p rows (corresponding to the fragments for the different
     compounds of the compounds file)
-  | Last column "corvalid" is a boolean for validated fragments 
+  | Last column "corvalid" is a boolean for validated fragments
 
 processing_file.pdf
-  | pdf output 
+  | pdf output
   | For each compound of the compounds file, Graph of the all fragments
     with parents (or most intense peak if parent is not detected in the
     fragments. At the end the pdf file a graph of the spectra with
@@ -103,7 +103,7 @@ Changelog/News
     mzref and the rtref to be the 1st, the 2nd and the 3rd columns
     respectively, and the header was somewhat ignored in the compound
     file.
-  | 
+  |
   | Now, we'd like to add some new columns, some of them are optional.
     This new
     format of file implies a better definition of the columns order,
@@ -114,7 +114,7 @@ Changelog/News
   |   - **elemcomposition** [OPTIONAL] ;
   |   - **mz** [MANDATORY] ;
   |   - **rtsec** [MANDATORY].
-  | 
+  |
   | These names can be written indiferentially in lower and/or upper
     case. The new definition being incompatible with the older one, that
     was more flexible, but also more error-prone.
@@ -139,7 +139,7 @@ Changelog/News
     </token>
 
     <token name="@TOOL_VERSION@">2.2.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
 
     <xml name="has_smol_stdout">
         <has_line line="processing 2-diethylamino-6-methyl pyrimidin-4-ol one" />
@@ -236,4 +236,4 @@ Changelog/News
         <has_line line=">> fragments: 77 79 81 82 83 85 88 89 91 92 93 95 96 97 99 101 103 105 106 107 108 109 110 111 113 114 115 117 118 119 121 125 127 129 131 133 135 137 138 139 140 141 142 143 145 147 148 149 153 154 155 156 159 161 163 165 167 169 171 172 173 174 175 177 178 179 181 183 184 185 186 187 191 193 195 196 197 198 199 200 201 203 205 209 211 212 213 214 215 219 221 222 224 225 226 227 228 229 236 239 240 241 243 248 256 257 258" />
     </xml>
 
-</macros>
+</macros>

tools/mzxmlshaper/mzXMLShaper.xml

@@ -1,4 +1,4 @@
-<tool id="mzxmlshaper" name="Mz(X)ML Shaper" version="1.0.0+galaxy0" profile="21.01">
+<tool id="mzxmlshaper" name="Mz(X)ML Shaper" version="1.0.0+galaxy1" profile="21.01">
   <description>
     conversion into XCMS-supported mz(X)ML file formats
   </description>
@@ -8,6 +8,9 @@
     <requirement type="package" version="2.36.0">bioconductor-mzr</requirement>
     <requirement type="package" version="1.0.0">r-w4mrutils</requirement>
   </requirements>
+  <required_files>
+    <include path="mzXMLShaper.R" />
+</required_files>
   <command detect_errors="aggressive"><![CDATA[
     Rscript '$__tool_directory__/mzXMLShaper.R'
       inputfilename '$infile'
@@ -111,23 +114,23 @@ A file (or collection of files) converted in mzML or mzXML with the same name as
 EXAMPLE OF WORKFLOW POSITION
 ----------------------------
 
-Used as first step in any workflow supporting mzML or mzXML formats just before ReadMSData. 
+Used as first step in any workflow supporting mzML or mzXML formats just before ReadMSData.
 
 ---------------------------------------------------
 
 ===============
 TOOL PARAMETERS
 ===============
 
-- Desired output format: mzML or MZXML 
+- Desired output format: mzML or MZXML
 
 ---------------------------------------------------
 
 ==================
 OUTPUT DESCRIPTION
 ==================
 
-Standardized MzML or mzXML files (depending on the user's configuration of the tool) 
+Standardized MzML or mzXML files (depending on the user's configuration of the tool)
 
 ---------------------------------------------------
 
@@ -142,10 +145,10 @@ KNOWN ISSUES
 ------------
 
 MzR does not read Bruker's DataAnalysis mzML or mzXML files, as they are not "standard" or "Pwiz-style" files (August 2024). This might also be the case for other constructor-converted mzML/mzXML, in that case an "unsupported file format" error will happen. However, this tool is functional for ProteoWizard's MSConvert mzML/mzXML files.
-    
+
   ]]>
   </help>
   <citations>
     <citation type="doi">10.18129/B9.bioc.mzR</citation>
   </citations>
-  </tool>
+  </tool>

tools/nmr_annotation/asics_xml.xml

@@ -1,11 +1,16 @@
-<tool id="NmrAnnotation" name="NMR_Annotation" version="3.0.0">
+<tool id="NmrAnnotation" name="NMR_Annotation" version="3.0.0+galaxy1">
 
     <description> Annotation of complex mixture NMR spectra and metabolite proportion estimation </description>
 
     <requirements>
         <requirement type="package" version="1.1_4">r-batch</requirement>
         <requirement type="package" version="1.0.1">r-asics</requirement>
     </requirements>
+    <required_files>
+        <include path="asics_wrapper.R" />
+        <include path="DrawSpec.R" />
+        <include path="Library.Rdata" />
+    </required_files>
 
     <stdio>
         <exit_code range="1:" level="fatal" />

tools/nmr_annotation2d/annotationRmn2D_xml.xml

@@ -1,4 +1,4 @@
-<tool id="2DNmrAnnotation" name="2DNMRAnnotation" version="2.0.0" profile="20.09">
+<tool id="2DNmrAnnotation" name="2DNMRAnnotation" version="2.0.0+galaxy1" profile="20.09">
 
     <description> Annotation of complex mixture bidimensional NMR spectra </description>
 
@@ -13,7 +13,18 @@
         <requirement type="package" version="1.6">r-jsonlite</requirement>
         <requirement type="package">r-stringi</requirement>
     </requirements>
-
+    <required_files>
+        <include path="annotationRmn2DWrapper.R" />
+        <include path="annotationRmn2D.R" />
+        <include path="annotationRmn2DGlobale.R" />
+        <include path="viridis.R" />
+        <include path="BdDReference_COSY.RData" />
+        <include path="BdDReference_HMBC.RData" />
+        <include path="BdDReference_HSQC.RData" />
+        <include path="BdDReference_JRES.RData" />
+        <include path="BdDReference_NOESY.RData" />
+        <include path="BdDReference_TOCSY.RData" />
+    </required_files>
     <stdio>
         <exit_code range="1:" level="fatal" />
     </stdio>

tools/nmr_preprocessing/NmrPreprocessing_xml.xml

@@ -1,4 +1,4 @@
-<tool id="NMR_Preprocessing" name="NMR_Preprocessing" version="@WRAPPER_VERSION@">
+<tool id="NMR_Preprocessing" name="NMR_Preprocessing" version="@WRAPPER_VERSION@+galaxy1">
     <description> Preprocessing of 1D NMR spectra </description>
 
     <macros>
@@ -9,6 +9,11 @@
         <requirement type="package" version="1.9_12">r-ptw</requirement>
         <requirement type="package" version="1.2_12">r-matrix</requirement>
     </expand>
+    <required_files>
+        <include path="NmrPreprocessing_wrapper.R" />
+        <include path="NmrPreprocessing_script.R" />
+        <include path="DrawFunctions.R" />
+    </required_files>
 
     <expand macro="stdio"/>
 

tools/nmr_preprocessing/ReadFids_xml.xml

@@ -1,11 +1,16 @@
-<tool id="NMR_Read" name="NMR_Read" version="@WRAPPER_VERSION@">
+<tool id="NMR_Read" name="NMR_Read" version="@WRAPPER_VERSION@+galaxy1">
     <description> Read Bruker NMR raw files</description>
 
     <macros>
         <import>macros.xml</import>
     </macros>
 
     <expand macro="requirements" />
+    <required_files>
+        <include path="ReadFids_wrapper.R" />
+        <include path="ReadFids_script.R" />
+        <include path="DrawFunctions.R" />
+    </required_files>
 
     <expand macro="stdio"/>