# HG changeset patch
# User jjohnson
# Date 1582752426 18000
# Node ID 153d5fa7af53fc9fde6a889efc8ca1887bd1a85a
# Parent  883cdf0ffae5370c73d434bf7ef7c610751b0bff
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"

diff -r 883cdf0ffae5 -r 153d5fa7af53 iedb_api.py
--- a/iedb_api.py	Wed Feb 26 15:02:37 2020 -0500
+++ b/iedb_api.py	Wed Feb 26 16:27:06 2020 -0500
@@ -5,9 +5,8 @@
 import re
 import sys
 import time
-
 from urllib.error import HTTPError
-from urllib.parse import urlencode, unquote
+from urllib.parse import unquote, urlencode
 from urllib.request import urlopen
 
 mhci_methods = ['recommended', 'consensus',
@@ -186,13 +185,13 @@
                             warn_err(msg, exit_code=1)
                         if line.find('eptide') > 0:
                             header = "#%s%s" %\
-                                    ("ID\t" if seqid else "", line)
+                                ("ID\t" if seqid else "", line)
                             if args.debug:
                                 print(header, file=sys.stderr)
                             continue
                         elif method == 'Bepipred' and line.find('Residue') > 0:
                             header2 = "#%s%s" %\
-                                    ("ID\t" if seqid else "", line)
+                                ("ID\t" if seqid else "", line)
                             if args.debug:
                                 print(header2, file=sys.stderr)
                             rslts = results2
diff -r 883cdf0ffae5 -r 153d5fa7af53 iedb_api.xml
--- a/iedb_api.xml	Wed Feb 26 15:02:37 2020 -0500
+++ b/iedb_api.xml	Wed Feb 26 16:27:06 2020 -0500
@@ -85,7 +85,7 @@
             -s $seq.strip()
           #end for
         #end if
-        -o $output
+        -o '$output'
     ]]></command>
     <inputs>
         <conditional name="prediction">
@@ -132,7 +132,7 @@
                     <option value="comblib">comblib</option>
                     <option value="tepitope">tepitope</option>
                 </param>
-                <expand macro="alleles" hla_regex="((DPA1\*0[1-3](:0[1-3])?/DPB1\*0[1-6]:0[12]|DQA1\*0[1-5]:0[12]/DQB1\*0[2-6]:0[12]|DRB[1-5]\*[01][1-9]:0[1-5]|H2-IA[bd]),(asis|[1-2][0-9]|30))*" hla_examples="DPA1*01/DPB1*04:01 HLA-DRB1*01:01 H2-IAb" hlalen_examples="DPA1*01/DPB1*04:01,11,15"/>
+                <expand macro="alleles" hla_regex="(DPA1\*0[1-3](:0[1-3])?/DPB1\*0[1-6]:0[12]|DQA1\*0[1-5]:0[12]/DQB1\*0[2-6]:0[12]|DRB[1-5]\*[01][1-9]:0[1-5]|H2-IA[bd])(,(asis|[1-2][0-9]|30))*" hla_examples="DPA1*01/DPB1*04:01 HLA-DRB1*01:01 H2-IAb" hlalen_examples="DPA1*01/DPB1*04:01,11,15"/>
                 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
                     <help>Used for any alleles which don't include specified lengths</help>
                     <option value="asis">asis</option>
@@ -225,7 +225,7 @@
                <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/>
            </when>
            <when value="entry">
-               <param name="seq_text" type="text" size="80" label="Peptide Sequence"/>
+               <param name="seq_text" type="text" label="Peptide Sequence"/>
            </when>
         </conditional>
 
@@ -405,10 +405,9 @@
 
 The RNAseq data for the subject would be used for:
 
-  - HLA prediction by seq2HLA_
+  - HLA prediction by seq2HLA
   - Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta 
 
-.. _seq2HLA: https://toolshed.g2.bx.psu.edu/view/iuc/seq2hla/52bba1cd3823
 
 .. image:: $PATH_TO_IMAGES/IEDB_Workflow_QueryTabular.png
    :width: 584
@@ -428,7 +427,7 @@
    :width: 74
    :height: 81
 
-In the workflow above QueryTabular_ tool converts the alleles:
+In the workflow above QueryTabular tool converts the alleles:
 
   - Filter Dataset Input
 
@@ -441,12 +440,8 @@
 
     * SELECT c1 FROM t1 UNION SELECT c2 FROM t1
 
-.. _QueryTabular: https://toolshed.g2.bx.psu.edu/view/iuc/query_tabular/0c95a3f1654f
 
-
-The IEDB formatting can also be performed by TextProcessing_ tools:
-
-.. _TextProcessing: https://toolshed.g2.bx.psu.edu/view/bgruening/text_processing/0a8c6b61f0f4
+The IEDB formatting can also be performed by TextProcessing tools:
 
 .. image:: $PATH_TO_IMAGES/TextProcessingConversion.png
    :width: 608