Fix profile and requirements

galaxyproteomics · Jul 3, 2024 · 371f840 · 371f840
1 parent 8bef62c
commit 371f840
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Showing 12 changed files with 21 additions and 57 deletions.
diff --git a/tools/cardinal/classification.xml b/tools/cardinal/classification.xml
@@ -1,12 +1,9 @@
-<tool id="cardinal_classification" name="MSI classification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="cardinal_classification" name="MSI classification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>spatial classification of mass spectrometry imaging data</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <!--requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="3.3.5">r-ggplot2</requirement-->
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
 

diff --git a/tools/cardinal/colocalization.xml b/tools/cardinal/colocalization.xml
@@ -1,11 +1,9 @@
-<tool id="cardinal_colocalization" name="MSI colocalization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="cardinal_colocalization" name="MSI colocalization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>mass spectrometry imaging colocalization</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="2.3">r-gridextra</requirement>
-      </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
     <![CDATA[
 

diff --git a/tools/cardinal/combine.xml b/tools/cardinal/combine.xml
@@ -1,15 +1,11 @@
-<tool id="cardinal_combine" name="MSI combine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="cardinal_combine" name="MSI combine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>
         combine several mass spectrometry imaging datasets into one
     </description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <!--requirement type="package" version="3.3.5">r-ggplot2</requirement>
-        <requirement type="package" version="0.12">r-maldiquantforeign</requirement>
-        <requirement type="package" version="1.20">r-maldiquant</requirement-->
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
     <![CDATA[
         #for $i, $infile in enumerate($infiles):

diff --git a/tools/cardinal/data_exporter.xml b/tools/cardinal/data_exporter.xml
@@ -1,4 +1,4 @@
-<tool id="cardinal_data_exporter" name="MSI data exporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="cardinal_data_exporter" name="MSI data exporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>
         exports imzML and Analyze7.5 to tabular files
     </description>

diff --git a/tools/cardinal/filtering.xml b/tools/cardinal/filtering.xml
@@ -1,12 +1,9 @@
-<tool id="cardinal_filtering" name="MSI filtering" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="cardinal_filtering" name="MSI filtering" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>tool for filtering mass spectrometry imaging data</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <!--requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="3.3.5">r-ggplot2</requirement-->
-    </expand>
+    <expand macro="requirements"/>
     <expand macro="print_version"/>
     <command detect_errors="exit_code">
     <![CDATA[

diff --git a/tools/cardinal/macros.xml b/tools/cardinal/macros.xml
@@ -5,7 +5,6 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-cardinal</requirement>
-            <!--requirement type="package" version="3.6.1">r-base</requirement-->
             <requirement type="package" version="2.3">r-gridextra</requirement>
             <requirement type="package" version="3.5.1">r-ggplot2</requirement>
             <requirement type="package" version="0.14.1">r-maldiquantforeign</requirement>

diff --git a/tools/cardinal/mz_images.xml b/tools/cardinal/mz_images.xml
@@ -1,13 +1,11 @@
-<tool id="cardinal_mz_images" name="MSI mz images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="cardinal_mz_images" name="MSI mz images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>
         mass spectrometry imaging m/z heatmaps
     </description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <!--requirement type="package" version="2.3">r-gridextra</requirement-->
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="aggressive">
 <![CDATA[
         @INPUT_LINKING@

diff --git a/tools/cardinal/preprocessing.xml b/tools/cardinal/preprocessing.xml
@@ -1,16 +1,11 @@
-<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>
         mass spectrometry imaging preprocessing
     </description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <!--requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="3.4.0">r-ggplot2</requirement>
-        <requirement type="package" version="3.50.0">bioconductor-sva</requirement>
-        <requirement type="package" version="1.1.0.1">r-randomcolor</requirement-->
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
     <![CDATA[
 

diff --git a/tools/cardinal/quality_report.xml b/tools/cardinal/quality_report.xml
@@ -1,18 +1,11 @@
-<tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>
         mass spectrometry imaging QC
     </description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <!--requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="3.3.5">r-ggplot2</requirement>
-        <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
-        <requirement type="package" version="2.23_20">r-kernsmooth</requirement>
-        <requirement type="package" version="1.1.1">r-scales</requirement>
-        <requirement type="package" version="1.0.12">r-pheatmap</requirement-->
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
     <![CDATA[
         @INPUT_LINKING@

diff --git a/tools/cardinal/segmentation.xml b/tools/cardinal/segmentation.xml
@@ -1,12 +1,9 @@
-<tool id="cardinal_segmentations" name="MSI segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="cardinal_segmentations" name="MSI segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>mass spectrometry imaging spatial clustering</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <!--requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="3.3.5">r-ggplot2</requirement-->
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
     <![CDATA[
 

diff --git a/tools/cardinal/spatial_DGMM.xml b/tools/cardinal/spatial_DGMM.xml
@@ -1,11 +1,9 @@
-<tool id="cardinal_single_ion_segmentation" name="MSI single ion segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="cardinal_single_ion_segmentation" name="MSI single ion segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>mass spectrometry imaging spatial DGMM</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <!--requirement type="package" version="2.3">r-gridextra</requirement-->
-      </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
     <![CDATA[
 

diff --git a/tools/cardinal/spectra_plots.xml b/tools/cardinal/spectra_plots.xml
@@ -1,15 +1,11 @@
-<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>
         mass spectrometry imaging mass spectra plots
     </description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <!--requirement type="package" version="3.3.5">r-ggplot2</requirement>
-        <requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="1.1.1">r-scales</requirement-->
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
     <![CDATA[
         @INPUT_LINKING@