From: Sorina Pop <sorina.pop@creatis.insa-lyon.fr>
Date: Fri, 18 Nov 2016 13:28:25 +0000 (+0100)
Subject: added options field and correct odinepiexe
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=8f641fa9b66ba2cec9983401990c5a4cf80a56b2;p=vip-workflow-odin.git

added options field and correct odinepiexe
---

diff --git a/bin/odin-release.tgz b/bin/odin-release.tgz
index ad7fb14..7fb33f1 100644
Binary files a/bin/odin-release.tgz and b/bin/odin-release.tgz differ
diff --git a/bin/odin.sh b/bin/odin.sh
index b761f60..089433f 100644
--- a/bin/odin.sh
+++ b/bin/odin.sh
@@ -72,6 +72,17 @@ PROPATH=$1
 SMPPATH=$2
 RESDIR=$3
 ODINSEQ=$4
+OPTIONS=$5
+
+if [ "${OPTIONS}" != "no" ] 
+then
+        OPT=`echo ${OPTIONS} | sed s/_/\ /g`
+else
+        OPT=""
+fi
+
+echo "Options are $OPT"
+
 
 PRO=`basename $PROPATH`
 SMP=`basename $SMPPATH`
@@ -109,8 +120,8 @@ else
 fi
 
 #launching program odinrecopexe
-echo "executing odinrecopexe -o $OUTNAME"
-./odinrecoexe -o $OUTNAME
+echo "executing odinrecopexe $OPT -o $OUTNAME"
+./odinrecoexe $OPT -o $OUTNAME
 
 CODE=$?
 if [ ${CODE} != 0 ]
diff --git a/gasw/odin.xml b/gasw/odin.xml
index fa74205..5942c11 100644
--- a/gasw/odin.xml
+++ b/gasw/odin.xml
@@ -16,6 +16,8 @@
                 </input>
 		<input name="odin_seq" option="no4">
                 </input>
+		<input name="options" option="no5">
+                </input>
                 <sandbox name="executable">
                         <access type="LFN" cached="true">
 
diff --git a/workflow/odin_epi.gwendia b/workflow/odin_epi.gwendia
index 7180ef1..f301f16 100644
--- a/workflow/odin_epi.gwendia
+++ b/workflow/odin_epi.gwendia
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<workflow name="odin" version="0.1">
+<workflow name="odin" version="0.2">
 
   <description>There is no description for this application. Please contact the developers to know what it is about.</description>
 
@@ -17,10 +17,15 @@
       </source-comment>
     </source>
     <constant name="OdinSeq" type="string" value="odinepiexe" cardinality="scalar" />
+    <source name="options" type="string">
+      <source-comment>&lt;b&gt;&lt;font color="blue"&gt;options&lt;/font&gt;&lt;/b&gt;: any option string, to be appended to the recon-all command line. For instance: '-all'. &lt;b&gt;Important:&lt;/b&gt; don't put spaces, use '_'  instead. And put 'no' in case you don't want to use any option.
+      </source-comment>
+    </source>
   </interface>
 
   <processors>
     <processor name="odin" >
+      <in name="input4" type="string" depth="0" />
       <in name="input3" type="string" depth="0" />
       <in name="input2" type="string" depth="0" />
       <in name="input1" type="uri" depth="0" />
@@ -31,6 +36,7 @@
           <port name="input1" />
           <port name="input2" />
           <port name="input3" />
+          <port name="input4" />
         </cross>
       </iterationstrategy>
       <gasw descriptor="[GASW_DIR]/odin.xml"/>
@@ -56,6 +62,7 @@ String result = dir.toString()+"/"+(dateFormat.format(System.currentTimeMillis()
       <link from="ResultsDirectory" to="append-date:dir" />
       <link from="append-date:result" to="odin:input2" />
       <link from="OdinSeq" to="odin:input3" />
+      <link from="options" to="odin:input4" />
   </links>
 
 </workflow>
diff --git a/workflow/odin_fisp.gwendia b/workflow/odin_fisp.gwendia
index f6d8204..10c862e 100644
--- a/workflow/odin_fisp.gwendia
+++ b/workflow/odin_fisp.gwendia
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<workflow name="odin" version="0.1">
+<workflow name="odin" version="0.2">
 
   <description>There is no description for this application. Please contact the developers to know what it is about.</description>
 
@@ -17,10 +17,15 @@
       </source-comment>
     </source>
     <constant name="OdinSeq" type="string" value="odinfispexe" cardinality="scalar" />
+    <source name="options" type="string">
+      <source-comment>&lt;b&gt;&lt;font color="blue"&gt;options&lt;/font&gt;&lt;/b&gt;: any option string, to be appended to the recon-all command line. For instance: '-all'. &lt;b&gt;Important:&lt;/b&gt; don't put spaces, use '_'  instead. And put 'no' in case you don't want to use any option.
+      </source-comment>
+    </source>
   </interface>
 
   <processors>
     <processor name="odin" >
+      <in name="input4" type="string" depth="0" />
       <in name="input3" type="string" depth="0" />
       <in name="input2" type="string" depth="0" />
       <in name="input1" type="uri" depth="0" />
@@ -31,6 +36,7 @@
           <port name="input1" />
           <port name="input2" />
           <port name="input3" />
+          <port name="input4" />
         </cross>
       </iterationstrategy>
       <gasw descriptor="[GASW_DIR]/odin.xml"/>
@@ -56,6 +62,7 @@ String result = dir.toString()+"/"+(dateFormat.format(System.currentTimeMillis()
       <link from="ResultsDirectory" to="append-date:dir" />
       <link from="append-date:result" to="odin:input2" />
       <link from="OdinSeq" to="odin:input3" />
+      <link from="options" to="odin:input4" />
   </links>
 
 </workflow>