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Several GTF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table.\n+    - name: format_of_annotation\n+      label: Format of the annotation file\n+      type: basic:string\n+      required: false\n+      default: GTF\n+      description: >\n+        Specify the format of the annotation file. GTF file is used by default.\n+    - name: count_multi_mapping_reads\n+      label: Count multi mapping reads\n+      type: basic:boolean\n+      required: false\n+      default: false\n+      description: >\n+        If specified, multi-mapping reads/fragments will be counted.\n+    - name: min_mqs\n+      label: Minimal mapping quality score\n+      type: basic:integer\n+      required: false\n+      default: 0\n+      description: >\n+        The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria.\n+    - name: strand_specific\n+      label: Strand specific read counting\n+      type: basic:integer\n+      required: false\n+      default: 0\n+      description: >\n+        Indicate if strand-specific read counting should be performed.\n+      choices:\n+        - label: unstranded\n+          value: 0\n+        - label: stranded\n+          value: 1\n+        - label: reversely stranded\n+          value: 2\n+    - name: feature_type\n+      label: Feature type\n+      type: basic:string\n+      default: exon\n+      description: >\n+        Feature type (3rd column in GFF file) to be used, all features of other type are ignored.\n+    - name: cpu_number\n+      label: Number of threads/CPUs\n+      type: basic:integer\n+      required: false\n+      default: 1\n+      description: >\n+        Specify the number of threads/CPUs used for mapping\n+    - name: PE_options\n+      label: Paired end alignment options\n+      group:\n+        - name: is_paired_end\n+          label: Is paired end\n+          type: basic:boolean\n+          required: false\n+          default: false\n+          description: >\n+            If specified, only fragments that have both ends successfully aligned will be considered for summarization.\n+        - name: require_both_ends_mapped\n+          label: Require both ends mapped\n+          type: basic:boolean\n+          required: false\n+          description: >\n+            If specified, only fragments that have both ends successfully aligned will be considered for summarization.\n+        - name: count_chimeric_fragments\n+          label: Count chimeric fragments\n+          type: basic:boolean\n+          required: false\n+          description: >\n+           If specified, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be counted.\n+  output:\n+    - name: featureCount_output\n+      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