--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_GFF_Features.xml	Mon May 09 08:26:30 2022 +0000
@@ -0,0 +1,114 @@
+<tool id="Extract_features1" name="Extract features" version="1.0.0">
+  <description>from GFF data</description>
+  <command interpreter="python">extract_GFF_Features.py $input1 $out_file1 ${column_choice.col} ${column_choice.feature}</command>
+  <inputs>
+    <param format="gff" name="input1" type="data" label="Select GFF data"/>
+    <conditional name="column_choice">
+      <param name="col" type="select" label="From">
+        <option value="0" selected="true">Column 1 / Sequence name</option>
+        <option value="1">Column 2 / Source</option>
+        <option value="2">Column 3 / Feature</option>
+        <option value="6">Column 7 / Strand</option>
+        <option value="7">Column 8 / Frame</option>
+      </param>
+      <when value="0">
+        <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
+          <options from_dataset="input1">
+            <column name="name" index="0"/>
+            <column name="value" index="0"/>
+            <filter type="unique_value" name="unique" column="0"/>
+          </options>
+        </param>
+      </when>
+      <when value="1">
+        <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
+          <options from_dataset="input1">
+            <column name="name" index="1"/>
+            <column name="value" index="1"/>
+            <filter type="unique_value" name="unique" column="1"/>
+          </options>
+        </param>
+      </when>
+      <when value="2">
+        <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
+          <options from_dataset="input1">
+            <column name="name" index="2"/>
+            <column name="value" index="2"/>
+            <filter type="unique_value" name="unique" column="2"/>
+          </options>
+        </param>
+      </when>
+      <when value="6">
+        <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
+          <options from_dataset="input1">
+            <column name="name" index="6"/>
+            <column name="value" index="6"/>
+            <filter type="unique_value" name="unique" column="6"/>
+          </options>
+        </param>
+      </when>
+      <when value="7">
+        <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
+          <options from_dataset="input1">
+            <column name="name" index="7"/>
+            <column name="value" index="7"/>
+            <filter type="unique_value" name="unique" column="7"/>
+          </options>
+        </param>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="input" name="out_file1" metadata_source="input1"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="5.gff"/>
+      <param name="col" value="0" />
+      <param name="feature" value="chr5,chr6,chr7,chr8" />
+      <output name="out_file1" file="Extract_features1_out.gff"/>
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+This tool extracts selected features from GFF data.
+
+-----
+
+**Example**
+
+Selecting **promoter** from the following GFF data::
+
+    chr22  GeneA  enhancer  10000000  10001000  500  +  .  TGA
+    chr22  GeneA  promoter  10010000  10010100  900  +  .  TGA
+    chr22  GeneB  promoter  10020000  10025000  400  -  .  TGB
+    chr22  GeneB  CCDS2220  10030000  10065000  800  -  .  TGB
+
+will produce the following output::
+
+    chr22  GeneA  promoter  10010000  10010100  900  +  .  TGA
+    chr22  GeneB  promoter  10020000  10025000  400  -  .  TGB
+
+----
+
+.. class:: infomark
+
+**About formats**
+
+**GFF format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields::
+
+    1. seqname - Must be a chromosome or scaffold.
+    2. source - The program that generated this feature.
+    3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
+    4. start - The starting position of the feature in the sequence. The first base is numbered 1.
+    5. end - The ending position of the feature (inclusive).
+    6. score - A score between 0 and 1000. If there is no score value, enter ".".
+    7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
+    8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
+    9. group - All lines with the same group are linked together into a single item.
+
+
+  </help>
+</tool>