--- a/iedb_api.xml	Wed Feb 26 16:27:06 2020 -0500
+++ b/iedb_api.xml	Fri Feb 28 15:45:14 2020 -0500
@@ -24,6 +24,7 @@
     <requirements>
         <requirement type="package" version="3.7">python</requirement>
     </requirements>
+
     <command detect_errors="exit_code"><![CDATA[
         #import re
         python '${__tool_directory__}/iedb_api.py' 
@@ -38,37 +39,9 @@
                 --proteasome $prediction.proteasome
             #end if
             #if $prediction.alleles.allelesrc == 'history':
-              #for $line in open(str($prediction.alleles.allele_file)):
-                #set $fields = $line.strip().split(',') 
-                #set $allele = $fields[0].strip()
-                #if len($allele) > 0:
-                  #if len($fields) > 1: 
-                    #for $alen in $fields[1:]:
-                      -a '$allele' -l $alen
-                    #end for
-                  #else:
-                    #for $alen in str($prediction.lengths).split(','):
-                      -a '$allele' -l $alen
-                    #end for
-                  #end if
-                #end if
-              #end for
+              -A '$prediction.alleles.allele_file'
             #else:
-              #for $word in str($prediction.alleles.allele_text).strip().split():
-                #set $fields = $word.strip().split(',') 
-                #set $allele = $fields[0].strip()
-                #if len($allele) > 0:
-                  #if len($fields) > 1: 
-                    #for $alen in $fields[1:]:
-                      -a '$allele' -l $alen
-                    #end for
-                  #else:
-                    #for $alen in str($prediction.lengths).split(','):
-                      -a '$allele' -l $alen
-                    #end for
-                  #end if
-                #end if
-              #end for
+              -A '$entered_alleles'
             #end if
         #end if
 
@@ -81,12 +54,33 @@
             -C #echo  int(str($sequence.id_col)) - 1
           #end if
         #else:
-          #for $seq in str($sequence.seq_text).strip().split():
-            -s $seq.strip()
-          #end for
+          -i '$entered_seqs' -c 1 -C 0
         #end if
         -o '$output'
     ]]></command>
+    <configfiles>     
+        <configfile name="entered_alleles"><![CDATA[#slurp
+#if $prediction.tool != 'bcell' and $prediction.alleles.allelesrc == 'entry'
+#for $word in str($prediction.alleles.allele_text).strip().split():
+#if $word.find(',') > 0
+$word
+#else
+#set $allele = $word + ',' + str($prediction.lengths)
+$allele
+#end if
+#end for
+#end if
+]]></configfile>     
+        <configfile name="entered_seqs"><![CDATA[#slurp
+#if $sequence.seqsrc == 'entry'
+#for $i, $seq in enumerate(str($sequence.seq_text).strip().split())
+#set $seqid = $i + 1
+#set $seqtext = '\t'.join([str($seqid),$seq.strip()])
+$seqtext
+#end for
+#end if
+]]></configfile>     
+    </configfiles>     
     <inputs>
         <conditional name="prediction">
             <param name="tool" type="select" label="Prediction">
@@ -132,7 +126,7 @@
                     <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]|(HLA-)?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>
@@ -382,6 +376,24 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- test8 -->
+        <test>
+            <conditional name="prediction">
+                <param name="tool" value="bcell"/>
+                <param name="method" value="Bepipred"/>
+                <param name="window_size" value="9"/>
+            </conditional>
+            <conditional name="sequence">
+                <param name="seqsrc" value="fasta"/>
+                <param name="seq_fasta" ftype="fasta" value="bcell.fa"/>
+            </conditional>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="ADVAGH" />
+                </assert_contents>
+            </output>
+        </test>
+
     </tests>
     <help><![CDATA[
 The IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases. It offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species.