From 986bd18e5bf77ec246b1d07b043b9ed7b57a30b9 Mon Sep 17 00:00:00 2001
From: Nirmayi <ynirmayi@gmail.com>
Date: Mon, 29 Jan 2024 17:30:46 +0100
Subject: [PATCH] move out of subreads directory and fix typos

---
 .../featurecounts/config.vsh.yaml             |  21 +++++++-----------
 src/{subread => }/featurecounts/help.txt      |   0
 src/{subread => }/featurecounts/script.sh     |   0
 src/{subread => }/featurecounts/test.sh       |   0
 .../featurecounts/test_data/a.bam             | Bin
 .../featurecounts/test_data/annotation.gtf    |   0
 .../featurecounts/test_data/genome.fasta      |   0
 .../featurecounts/test_data/script.sh         |   0
 8 files changed, 8 insertions(+), 13 deletions(-)
 rename src/{subread => }/featurecounts/config.vsh.yaml (97%)
 rename src/{subread => }/featurecounts/help.txt (100%)
 rename src/{subread => }/featurecounts/script.sh (100%)
 rename src/{subread => }/featurecounts/test.sh (100%)
 rename src/{subread => }/featurecounts/test_data/a.bam (100%)
 rename src/{subread => }/featurecounts/test_data/annotation.gtf (100%)
 rename src/{subread => }/featurecounts/test_data/genome.fasta (100%)
 rename src/{subread => }/featurecounts/test_data/script.sh (100%)

diff --git a/src/subread/featurecounts/config.vsh.yaml b/src/featurecounts/config.vsh.yaml
similarity index 97%
rename from src/subread/featurecounts/config.vsh.yaml
rename to src/featurecounts/config.vsh.yaml
index e683b5a3..f7fa1a04 100644
--- a/src/subread/featurecounts/config.vsh.yaml
+++ b/src/featurecounts/config.vsh.yaml
@@ -1,5 +1,5 @@
 functionality: 
-  name: subread_featurecounts
+  name: featurecounts
   description: |
     featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications.
   info:
@@ -22,7 +22,7 @@ functionality:
           description: | 
             Name of an annotation file. GTF/GFF format by default. See -F option for more format information.
           required: true
-          examples: annotation.gtf
+          example: annotation.gtf
         - name: --input
           alternatives: ["-i"]
           type: file
@@ -31,31 +31,31 @@ functionality:
           description: |
             A comma-separated list of SAM or BAM format files. They can be either name or location sorted. Location-sorted paired-end reads are automatically sorted by read names.
           required: true
-          examples: input_file1.bam
+          example: input_file1.bam
     
     - name: Outputs
       arguments:
         - name: --output
-          alternative: ["-o"]
+          alternatives: ["-o"]
           type: file
           direction: output
           description: | 
             Name of output file including read counts. A separate file including summary statistics of counting results is also included in the output ('<output>.summary'). Both files are in tab delimited format.
-          required: true
+          must_exist: true
           example: features.txt
         - name: --output_summary
           type: file
           direction: output
           description: | 
             Summary statistics of counting results is also included in the output ('<output>.summary'). 
-          required: true
+          must_exist: true
           example: features.txt.summary
         - name: --output_junctions
           type: file
           direction: output
           description: | 
             Count of number of reads supporting each exon-exon junction. See -J for more information.
-          required: false
+          must_exist: false
           example: features.txt.jcounts
           must_exist: false
         - name: --r_path
@@ -63,7 +63,7 @@ functionality:
           direction: output
           description: | 
             Directory to save the detailed assignment results. If unspecified, the directory where counting results are saved is used. See -R for more format information.
-          required: false
+          must_exist: false
           example: detailed_results/
           must_exist: false
 
@@ -325,11 +325,6 @@ functionality:
           type: boolean_true
           description: | 
             Output verbose information for debugging, such as un-matched chromosome/contig names.
-        - name: --version
-          alternatives: ["-v"]
-          type: boolean_true
-          description: | 
-            Output version of the program.
   
   resources:
     - type: bash_script
diff --git a/src/subread/featurecounts/help.txt b/src/featurecounts/help.txt
similarity index 100%
rename from src/subread/featurecounts/help.txt
rename to src/featurecounts/help.txt
diff --git a/src/subread/featurecounts/script.sh b/src/featurecounts/script.sh
similarity index 100%
rename from src/subread/featurecounts/script.sh
rename to src/featurecounts/script.sh
diff --git a/src/subread/featurecounts/test.sh b/src/featurecounts/test.sh
similarity index 100%
rename from src/subread/featurecounts/test.sh
rename to src/featurecounts/test.sh
diff --git a/src/subread/featurecounts/test_data/a.bam b/src/featurecounts/test_data/a.bam
similarity index 100%
rename from src/subread/featurecounts/test_data/a.bam
rename to src/featurecounts/test_data/a.bam
diff --git a/src/subread/featurecounts/test_data/annotation.gtf b/src/featurecounts/test_data/annotation.gtf
similarity index 100%
rename from src/subread/featurecounts/test_data/annotation.gtf
rename to src/featurecounts/test_data/annotation.gtf
diff --git a/src/subread/featurecounts/test_data/genome.fasta b/src/featurecounts/test_data/genome.fasta
similarity index 100%
rename from src/subread/featurecounts/test_data/genome.fasta
rename to src/featurecounts/test_data/genome.fasta
diff --git a/src/subread/featurecounts/test_data/script.sh b/src/featurecounts/test_data/script.sh
similarity index 100%
rename from src/subread/featurecounts/test_data/script.sh
rename to src/featurecounts/test_data/script.sh