Merge branch 'main' into bump-jquery

.github/workflows/planemo.yml

@@ -0,0 +1,91 @@
+name: Python CI/Planemo
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Cache Python packages
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-py${{ matrix.python-version }}
+          restore-keys: |
+            ${{ runner.os }}-pip-py
+      - name: Install dependencies
+        run: pip install flake8 flake8-import-order planemo Pygments
+      - name: Check dependencies
+        run: planemo --version
+      - name: Lint with planemo & flake8
+        run: planemo lint
+      - name: Shed lint with planemo
+        run: planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive .
+
+  test:
+    needs: [ lint ]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Cache Python packages
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-py${{ matrix.python-version }}
+          restore-keys: |
+            ${{ runner.os }}-pip-py
+      - name: Cache .planemo
+        uses: actions/cache@v4
+        with:
+          path: ~/.planemo
+          key: ${{ runner.os }}-planemo-py${{ matrix.python-version }}
+          restore-keys: |
+            ${{ runner.os }}-planemo-py
+      - name: Install Planemo
+        run: pip install Planemo
+      - name: Check Planemo version
+        run: planemo --version
+      - name: Run tests
+        run: planemo test
+
+  deploy:
+    if: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags/') }}
+    needs: [ test ]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Cache Python packages
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-py${{ matrix.python-version }}
+          restore-keys: |
+            ${{ runner.os }}-pip-py
+      - name: Install dependencies
+        run: pip install flake8 flake8-import-order planemo Pygments
+      - name: Check dependencies
+        run: planemo --version
+      - name: Deploy
+        run: planemo shed_update --shed_target toolshed --shed_key_from_env ${{ secrets.SHED_KEY }} --force_repository_creation .

CLIFinder.xml

@@ -201,19 +201,19 @@ perl '$__tool_directory__/script/CLIFinder.pl'
                 <when value="false" />
             </conditional>
         </section>
-        <param argument="--rmsk" name="rmsk" type="data" format="tabular" label="Tab-delimited text file (with headers) containing reference repeat sequences (e.g. rmsk track from UCSC)"/>
-        <param argument="--refseq" name="refseq" type="data" format="tabular" label="Tab-delimited file (with headers) containing reference genes (e.g. RefGene.txt from UCSC)"/>
+        <param argument="--rmsk" type="data" format="tabular" label="Tab-delimited text file (with headers) containing reference repeat sequences (e.g. rmsk track from UCSC)"/>
+        <param argument="--refseq" type="data" format="tabular" label="Tab-delimited file (with headers) containing reference genes (e.g. RefGene.txt from UCSC)"/>
         <param name="BDir" type="select" >
             <option value="0">Undirectional libraries</option>
             <option value="1">TEs sequences in first read in pair</option>
             <option value="2">TEs sequences in second read in pair</option>
         </param>
         <param argument="--size_read" name="size" type="integer" value="100" label="Reads size"/>
-        <param argument="--size_insert" name="size_insert" type="integer" value="250" label="Maximum insert size (bp)"/>
-        <param argument="--min_L1" name="min_L1" type="integer" value="50" label="Minimun bp mapping on selected TEs database"/>
-        <param argument="--mis_L1" name="mis_L1" type="integer" value="1" label="Number of mismatches tolerated in TEs mapping sequences"/>
-        <param argument="--min_unique" name="min_unique" type="integer" value="33" label="Minimum consecutive bp corresponding to a unique sequence"/>
-        <param argument="--species" name="species" type="text" value="human" label="Species or clade of the input sequence (the species name must be a valid NCBI Taxonomy Database species name and be contained in the RepeatMasker repeat database)"/>
+        <param argument="--size_insert" type="integer" value="250" label="Maximum insert size (bp)"/>
+        <param argument="--min_L1" type="integer" value="50" label="Minimun bp mapping on selected TEs database"/>
+        <param argument="--mis_L1" type="integer" value="1" label="Number of mismatches tolerated in TEs mapping sequences"/>
+        <param argument="--min_unique" type="integer" value="33" label="Minimum consecutive bp corresponding to a unique sequence"/>
+        <param argument="--species" type="text" value="human" label="Species or clade of the input sequence (the species name must be a valid NCBI Taxonomy Database species name and be contained in the RepeatMasker repeat database)"/>
     </inputs>
     <outputs>
         <data format="html" name="chimerae" label="${tool.name}_on_${on_string}"/>