add doc

docs/index.rst

@@ -103,6 +103,7 @@ Contents
    tools/agat_sp_manage_functional_annotation.md
    tools/agat_sp_manage_introns.md
    tools/agat_sp_merge_annotations.md
+   tools/agat_sp_move_attributes_within_records
    tools/agat_sp_prokka_fix_fragmented_gene_annotations.md
    tools/agat_sp_sensitivity_specificity.md
    tools/agat_sp_separate_by_record_type.md

docs/tools/agat_sp_move_attributes_within_records.md

@@ -0,0 +1,67 @@
+# NAME
+
+agat\_sp\_move\_attributes\_within\_records.pl
+
+# DESCRIPTION
+
+The script aims to keep move attributes within a record e.g. from Level1 to Level2 and/or Level3 features; and / or from Level2 to Level2 or Level3 features; and / or from Level3 to Level3 features.
+Example of L1 feature: gene
+Example of L2 featrue
+
+# SYNOPSIS
+
+```
+agat_sp_move_attributes_within_records.pl --gff infile.gff --feature_copy mRNA  --feature_paste CDS --attribute Dbxref,Ontology [ --output outfile ]
+agat_sp_move_attributes_within_records.pl --help
+```
+
+# OPTIONS
+
+- **-f**, **--reffile**, **--gff**  or **-ref**
+
+    Input GFF3 file that will be read
+
+- **--feature\_copy** or **--fc**
+
+    primary tag (feature type) option to list from which feature we will copy the attributes, case insensitive. 
+    You can specified a feature (or a coma separated list) by giving its primary tag / feature type (column 3) value as: cds, Gene, MrNa, etc
+    You can specify directly all the feature of a particular level:
+          level2=mRNA,ncRNA,tRNA,etc
+          level3=CDS,exon,UTR,etc
+    By default all level2 feature are used. 
+
+- **--feature\_paste** or **--fp**
+
+    primary tag (feature type) option to list to which feature we will paste the attributes, case sensitive. 
+    You can specified a feature (or a coma separated list) by giving its primary tag / feature type (column 3) value as: cds, Gene, MrNa, etc
+    You can specify directly all the feature of a particular level:
+          level2=mRNA,ncRNA,tRNA,etc
+          level3=CDS,exon,UTR,etc
+    By default all feature level3 are used. 
+
+- **-a** or **--attribute**
+
+    Attribute that will be copied and pasted. Case sensitive.
+    You can specified an attribute (or a coma separated list) by giving its attribute tag value (column9) as: Ontology, Dbxref, etc
+    Default: all\_attributes
+    /!\\ <all\_attributes> is a specific parameter meaning all the attributes will be use.
+
+- **-o** or **--output**
+
+    Output GFF file.  If no output file is specified, the output will be
+    written to STDOUT.
+
+- **-v**
+
+    Verbose option for debugging purpose.
+
+- **-c** or **--config**
+
+    String - Input agat config file. By default AGAT takes as input agat\_config.yaml file from the working directory if any, 
+    otherwise it takes the orignal agat\_config.yaml shipped with AGAT. To get the agat\_config.yaml locally type: "agat config --expose".
+    The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+
+- **-h** or **--help**
+
+    Display this helpful text.
+