v1.28.0+galaxy1 (Galaxy tool fixes for purityX and purityA) - doc update

.github/workflows/pr.yaml

@@ -35,18 +35,18 @@ jobs:
       run: echo "GALAXY_HEAD_SHA=$(git ls-remote ${{ env.GALAXY_REPO }} refs/heads/${{ env.GALAXY_RELEASE }} | cut -f1)" >> $GITHUB_ENV
     - name: Save latest galaxy commit to artifact file
       run: echo $GALAXY_HEAD_SHA > galaxy.sha
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
         name: Workflow artifacts
         path: galaxy.sha
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
     - name: Cache .planemo
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-planemo
       with:
         path: ~/.planemo
@@ -63,7 +63,7 @@ jobs:
       run: |
         touch tool.xml
         PIP_QUIET=2 planemo test --galaxy_python_version ${{ matrix.python-version }} --no_conda_auto_init --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
     # The range of commits to check for changes is:
@@ -88,7 +88,7 @@ jobs:
       run: planemo ci_find_repos --changed_in_commit_range $COMMIT_RANGE --exclude packages --exclude deprecated --exclude_from .tt_skip --output changed_repositories.list
     - name: Show repo list
       run: cat changed_repositories.list
-    - uses: actions/upload-artifact@v2.0.1
+    - uses: actions/upload-artifact@v3
       with:
         name: Workflow artifacts
         path: changed_repositories.list
@@ -105,20 +105,20 @@ jobs:
     steps:
     # checkout the repository
     # and use it as the current working directory
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v3
       with:
         name: Workflow artifacts
         path: ../workflow_artifacts/
     - name: Determine latest galaxy commit
       run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -144,20 +144,20 @@ jobs:
     steps:
     # checkout the repository to master
     # and use it as the current working directory
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v3
       with:
         name: Workflow artifacts
         path: ../workflow_artifacts/
     - name: Determine latest galaxy commit
       run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -200,7 +200,7 @@ jobs:
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v3
       with:
         name: Workflow artifacts
         path: ../workflow_artifacts/
@@ -267,7 +267,7 @@ jobs:
       run: |
         mkdir upload
         mv tool_test_output.json tool_test_output.html upload/
-    - uses: actions/upload-artifact@v2.0.1
+    - uses: actions/upload-artifact@v3
       with:
         name: 'Tool test output ${{ matrix.chunk  }}'
         path: upload
@@ -286,7 +286,7 @@ jobs:
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v3
       with:
         path: artifacts
     - uses: actions/setup-python@v1
@@ -295,7 +295,7 @@ jobs:
     - name: Determine latest galaxy commit
       run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -312,7 +312,7 @@ jobs:
       run: |
         mkdir upload
         mv tool_test_output.json tool_test_output.html upload/
-    - uses: actions/upload-artifact@v2.0.1
+    - uses: actions/upload-artifact@v3
       with:
         name: 'All tool test results'
         path: upload
@@ -333,20 +333,20 @@ jobs:
     runs-on: ubuntu-latest
     if: github.ref == 'refs/heads/master' && github.repository_owner == 'computational-metabolomics'
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v3
       with:
         name: Workflow artifacts
         path: ../workflow_artifacts/
     - name: Determine latest galaxy commit
       run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-pip
       with:
         path: ~/.cache/pip

README.rst

@@ -3,13 +3,13 @@ msPurity for Galaxy
 |Git| |Bioconda| |License|
 
 
-Version v1.28.0+galaxy0
+Version v1.28.0+galaxy1
 ------------------------
 
   - msPurity
      - bioconductor-mspurity v1.28.0
   - Galaxy tools
-     - v0
+     - v1
 
 About
 ------
@@ -52,6 +52,10 @@ Authors, contributors & contacts
 
 Changes
 -------------------------
+v1.28.0-galaxy1
+  - Further fix for purityX galaxy tool (https://github.com/computational-metabolomics/mspurity-galaxy/issues/53) 
+  - Fix for purityA file naming (https://github.com/computational-metabolomics/mspurity-galaxy/issues/56)
+
 v1.28.0-galaxy0
   - Version bump to v1.28.0
   - createMSP now uses the median precursor MZ and precursor RT in the MSP files

tools/msPurity/macros.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.28.0</token>
-    <token name="@GALAXY_TOOL_VERSION@">0</token>
+    <token name="@GALAXY_TOOL_VERSION@">1</token>
 
     <xml name="requirements">
         <requirements>

tools/msPurity/purityA.R

@@ -124,7 +124,7 @@ if (!is.null(opt$galaxy_names)) {
 print(pa)
 save(pa, file = file.path(opt$out_dir, "purityA_output.RData"))
 
-pa@puritydf$filename <- sapply(pa@puritydf$fileid, function(x) names(pa@fileList)[as.integer(x)])
+pa@puritydf$filename <- sapply(as.character(pa@puritydf$fileid), function(x) names(pa@fileList)[as.integer(x)])
 
 print(head(pa@puritydf))
 write.table(pa@puritydf, file.path(opt$out_dir, "purityA_output.tsv"), row.names = FALSE, sep = "\t")

tools/msPurity/purityX.R

@@ -16,7 +16,6 @@ option_list <- list(
   make_option("--singleFile", default = 0),
   make_option("--cores", default = 4),
   make_option("--xgroups", type = "character"),
-  make_option("--rdata_name", default = "xset"),
   make_option("--camera_xcms", default = "xset"),
   make_option("--files", type = "character"),
   make_option("--galaxy_files", type = "character"),
@@ -63,10 +62,10 @@ if (is.null(opt$rtraw_columns)) {
   rtraw_columns <- TRUE
 }
 
-loadRData <- function(rdata_path, xset_name) {
+loadRData <- function(rdata_path, xnames) {
   # loads an RData file, and returns the named xset object if it is there
   load(rdata_path)
-  return(get(ls()[ls() == xset_name]))
+  return(get(ls()[ls() %in% xnames]))
 }
 
 
@@ -90,7 +89,7 @@ getxcmsSetObject <- function(xobject) {
   }
 }
 
-target_obj <- loadRData(opt$xset_path, opt$rdata_name)
+target_obj <- loadRData(opt$xset_path, c('xset', 'xa', 'xdata'))
 
 if (opt$camera_xcms == "camera") {
   xset <- target_obj@xcmsSet

tools/msPurity/purityX.xml

@@ -18,11 +18,7 @@
                 --xgroups='$xgroups.xgroups_value'
             #end if
             --camera_xcms=$camera_xcms
-            #if $camera_xcms == "camera"
-                --rdata_name=xa
-            #else
-                --rdata_name=xset
-            #end if
+
             --iwNorm=$iw_norm
             --ilim=$ilim
             #if $isotopes.isotopes == "exclude_default"
@@ -121,10 +117,10 @@
         <expand macro="camera_xcms" />
 
         <param argument="--raw_rt_columns" type="boolean" label="Has the raw retention time been tracked within the peaks?"
-               help="Only applicable when using retention time correction with obiwarp. When obiwarp is used
-                     the retention time correction tracking is slightly different to the other correction methods. To ensure
-                     correct tracking with obiwarp an additional tool (track_rt_raw) should be performed prior to
-                     any retention time correction."/>
+               help="[Deprecated] No longer applicable. Previously when obiwarp was used
+                     the retention time correction tracking was slightly different to the other correction methods. To ensure
+                     correct tracking with obiwarp an additional tool (track_rt_raw) was performed prior to
+                     any retention time correction - and this was then checked when this flag was turned on"/>
 
         <expand macro="fileload" />