changeset 0:ef67bbb84e6b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/anarci_wrapper.xml	Mon Mar 29 10:44:57 2021 +0000
@@ -0,0 +1,117 @@
+<tool id="ANARCI" name="ANARCI" version="1.0">
+  <description>Use ANARCUI tools to use HADDOCK-antibody-antigen after.</description>
+  <command detect_errors="exit_code"><![CDATA[
+    conda activate Ab-HADDOCK;
+    python2.7 ImmunoPDB.py -i '${input}' -o '${output}' --scheme ${scheme} --splitscfv
+    #if $receptor
+      --receptor ${receptor}
+    #end if;
+    #if $fvonly
+      --fvonly
+    #end if;
+    #if $rename
+      --rename
+    #end if;
+    #if $splitscfv
+      --splitscfv
+    #end if;
+    conda deactivate
+  ]]></command>
+  <inputs>
+    <param format="pdb" name="input" type="data" label="Select your PDB file."/>
+    <param name="scheme" type="select" label="Scheme to use - default is 'IMGT'" help="Which numbering scheme should be used.">
+      <option value="imgt" selected="true">IMGT</option>
+      <option value="kabat">Kabat</option>
+      <option value="aho">Aho</option>
+      <option value="wolfguy">Wolfguy</option>
+      <option value="chothia">Chothia</option>
+      <option value="martin">Martin</option>
+      <option value="pdb">PDB</option>
+    </param>
+    <param name="receptor" type="select" optional="true" label="Choose ig or tr domains" help="Choose whether to number Antibody (ig) or TCR (tr) domains. (Optional)">
+      <option value="ig" >Antibody domains</option>
+      <option value="tr" >TCR domains</option>
+    </param>
+    <param name="fvonly" optional="true" label="Only output Fv regions." help="Only output Fv regions."/>
+    <param name="rename" optional="true" label="Rename the receptor chains." help="Rename the receptor chains with H and L (ig) or B and A (tr). Only receptor chains output. First pair identified used."/>
+    <param name="splitscfv" optional="true" label="Split chain." help="When they are found split single chain fvs into two seperate chains (fvonly becomes true)."/>
+  </inputs>
+  <outputs>
+    <data name="output" format="pdb" />
+  </outputs>
+  <help>
+usage: ImmunoPDB [-h] [-i INPUTSTRUCTURE] [-o OUTFILE]
+                 [--scheme {kabat,aho,wolfguy,imgt,a,c,chothia,i,k,m,w,martin,pdb}]
+                 [--receptor {ig,tr}] [--rename] [--fvonly] [--splitscfv]
+                 [--warnings]
+
+ANARCI - ImmunoPDB                                     \\    //
+Antibody Numbering and Antigen Receptor ClassIfication  \\  //
+                                                          ||
+(c) Oxford Protein Informatics Group (OPIG). 2015-16      ||
+
+Example script to number Antibody and TCR PDB structures.
+
+ANARCI must be installed and in the path
+opig.stats.ox.ac.uk/webapps/anarci
+
+Requirements: Biopython (version >= 1.66)
+              Muscle
+
+This script extends the BioPython PDBParser and Structure classes so that a numbering scheme can be applied to the variable domain
+of an antigen receptor chain. 
+
+o Where available the Seqres record is used as the full sequence. Missing residues are recognised by comparing this to the residues
+  with coordinates.
+
+o *Only* variable domains are numbered consistently in the chosen scheme.
+
+o Residues before the domain are numbered '0' with reverse alphabetical insertions if there are less than 28 (all 0 otherwise - this
+  will break some PDB parsers...)
+
+o Residues after the variable domain are numbered sequentially from 1001.
+
+o By default when more than one variable domain is found on a single chain (e.g. single chain Fv, diabody...) the numbering will be
+  with respect to the first domain identified.
+
+o CDR recognition is performed and regions are annotated in the xtra dictionary attributes of residue objects.
+
+o Pairing is performed using the distance between the interface cysteine positions (imgt 104).
+
+Basic useage
+
+Renumber antibody chains with imgt numbering scheme
+python ImmunoPDB.py -i infile.pdb -o outfile.pdb -s imgt
+
+Renumber tcr chains with imgt numbering scheme
+python ImmunoPDB.py -i infile.pdb -o outfile.pdb -s imgt --receptor tr
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -i INPUTSTRUCTURE     A structure to be numbered
+  -o OUTFILE            The output file to use. Default is stdout
+  --scheme {kabat,aho,wolfguy,imgt,a,c,chothia,i,k,m,w,martin,pdb}, -s {kabat,aho,wolfguy,imgt,a,c,chothia,i,k,m,w,martin,pdb}
+                        Which numbering scheme should be used. i, k, c, m, w
+                        and a are shorthand for IMGT, Kabat, Chothia, Martin
+                        (Extended Chothia), Wolfguy and Aho respectively.
+                        Default IMGT. Use pdb to retain the numbering but get
+                        the annotations as remarks
+  --receptor {ig,tr}, -r {ig,tr}
+                        Choose whether to number Antibody (ig) or TCR (tr)
+                        domains.
+  --rename              Rename the receptor chains with H and L (ig) or B and
+                        A (tr). Only receptor chains output. First pair
+                        identified used.
+  --fvonly              Only output Fv regions.
+  --splitscfv           When they are found split single chain fvs into two
+                        seperate chains (fvonly becomes true)
+  --warnings            Report warnings about missing residues
+
+Author: James Dunbar ([e-mail])
+        Charlotte Deane ([e-mail])
+
+Copyright (C) 2016 Oxford Protein Informatics Group (OPIG)
+Freely distributed under the GNU General Public License (GPLv3).
+  </help>
+</tool>
+