Attempt to be robust to not having an alignment in our RunXml file
[htsworkflow.git] / docs / gaworkflow.xmi
1 <?xml version="1.0" encoding="UTF-8"?>
2 <XMI xmlns:UML="http://schema.omg.org/spec/UML/1.3" verified="false" timestamp="2008-01-11T15:30:52" xmi.version="1.2" >
3  <XMI.header>
4   <XMI.documentation>
5    <XMI.exporter>umbrello uml modeller http://uml.sf.net</XMI.exporter>
6    <XMI.exporterVersion>1.5.8</XMI.exporterVersion>
7    <XMI.exporterEncoding>UnicodeUTF8</XMI.exporterEncoding>
8   </XMI.documentation>
9   <XMI.metamodel xmi.name="UML" href="UML.xml" xmi.version="1.3" />
10  </XMI.header>
11  <XMI.content>
12   <UML:Model isSpecification="false" isLeaf="false" isRoot="false" xmi.id="m1" isAbstract="false" name="UML Model" >
13    <UML:Namespace.ownedElement>
14     <UML:Stereotype isSpecification="false" isLeaf="false" visibility="public" namespace="m1" xmi.id="folder" isRoot="false" isAbstract="false" name="folder" />
15     <UML:Stereotype isSpecification="false" isLeaf="false" visibility="public" namespace="m1" xmi.id="datatype" isRoot="false" isAbstract="false" name="datatype" />
16     <UML:Model stereotype="folder" isSpecification="false" isLeaf="false" visibility="public" namespace="m1" xmi.id="Logical View" isRoot="false" isAbstract="false" name="Logical View" >
17      <UML:Namespace.ownedElement>
18       <UML:Package stereotype="folder" isSpecification="false" isLeaf="false" visibility="public" namespace="Logical View" xmi.id="Datatypes" isRoot="false" isAbstract="false" name="Datatypes" >
19        <UML:Namespace.ownedElement>
20         <UML:DataType stereotype="datatype" isSpecification="false" isLeaf="false" visibility="public" namespace="Datatypes" xmi.id="zHGiO7QUZRiX" isRoot="false" isAbstract="false" name="int" />
21         <UML:DataType stereotype="datatype" isSpecification="false" isLeaf="false" visibility="public" namespace="Datatypes" xmi.id="LzF7NnxDIQZy" isRoot="false" isAbstract="false" name="char" />
22         <UML:DataType stereotype="datatype" isSpecification="false" isLeaf="false" visibility="public" namespace="Datatypes" xmi.id="rF1bLfYctE0z" isRoot="false" isAbstract="false" name="bool" />
23         <UML:DataType stereotype="datatype" isSpecification="false" isLeaf="false" visibility="public" namespace="Datatypes" xmi.id="eTY593cV1paM" isRoot="false" isAbstract="false" name="float" />
24         <UML:DataType stereotype="datatype" isSpecification="false" isLeaf="false" visibility="public" namespace="Datatypes" xmi.id="dYZty7spMrOf" isRoot="false" isAbstract="false" name="double" />
25         <UML:DataType stereotype="datatype" isSpecification="false" isLeaf="false" visibility="public" namespace="Datatypes" xmi.id="UuHO7GNlhtpq" isRoot="false" isAbstract="false" name="short" />
26         <UML:DataType stereotype="datatype" isSpecification="false" isLeaf="false" visibility="public" namespace="Datatypes" xmi.id="xPJyEuIpQpjO" isRoot="false" isAbstract="false" name="long" />
27         <UML:DataType stereotype="datatype" isSpecification="false" isLeaf="false" visibility="public" namespace="Datatypes" xmi.id="wZCGOYvqRDEY" isRoot="false" isAbstract="false" name="unsigned int" />
28         <UML:DataType stereotype="datatype" isSpecification="false" isLeaf="false" visibility="public" namespace="Datatypes" xmi.id="RZH8T4yOTGKi" isRoot="false" isAbstract="false" name="unsigned short" />
29         <UML:DataType stereotype="datatype" isSpecification="false" isLeaf="false" visibility="public" namespace="Datatypes" xmi.id="AcXaREwMl6c9" isRoot="false" isAbstract="false" name="unsigned long" />
30         <UML:DataType stereotype="datatype" isSpecification="false" isLeaf="false" visibility="public" namespace="Datatypes" xmi.id="dYy4jCaAkpGB" isRoot="false" isAbstract="false" name="string" />
31        </UML:Namespace.ownedElement>
32       </UML:Package>
33       <UML:Class isSpecification="false" isLeaf="false" visibility="public" namespace="Logical View" xmi.id="lZR99u8H0ec9" isRoot="false" isAbstract="false" name="SpoolWatcher" />
34       <UML:Class isSpecification="false" isLeaf="false" visibility="public" namespace="Logical View" xmi.id="GkJy5VAr2ZyC" isRoot="false" isAbstract="false" name="Copier" >
35        <UML:Classifier.feature>
36         <UML:Operation isSpecification="false" isLeaf="false" visibility="public" xmi.id="74kpdjSI8Fmc" isRoot="false" isAbstract="false" isQuery="false" name="startCopy" />
37         <UML:Operation isSpecification="false" isLeaf="false" visibility="public" xmi.id="ZEGJnJU2LB4i" isRoot="false" isAbstract="false" isQuery="false" name="sequencingFinished" >
38          <UML:BehavioralFeature.parameter>
39           <UML:Parameter isSpecification="false" visibility="private" xmi.id="0F6mtJp0LYow" value="" type="dYy4jCaAkpGB" name="runDir" />
40          </UML:BehavioralFeature.parameter>
41         </UML:Operation>
42        </UML:Classifier.feature>
43       </UML:Class>
44       <UML:Class isSpecification="false" isLeaf="false" visibility="public" namespace="Logical View" xmi.id="0UoIUrhibyff" isRoot="false" isAbstract="false" name="Runner" >
45        <UML:Classifier.feature>
46         <UML:Operation isSpecification="false" isLeaf="false" visibility="public" xmi.id="t3UPqTGoZoip" isRoot="false" isAbstract="false" isQuery="false" name="sequencingFinished" >
47          <UML:BehavioralFeature.parameter>
48           <UML:Parameter isSpecification="false" visibility="private" xmi.id="RRzKx8Z14iIF" value="" type="dYy4jCaAkpGB" name="runDir" />
49          </UML:BehavioralFeature.parameter>
50         </UML:Operation>
51         <UML:Operation isSpecification="false" isLeaf="false" visibility="public" xmi.id="4yuLbdrUeJtU" isRoot="false" isAbstract="false" isQuery="false" name="pipelineFinished" >
52          <UML:BehavioralFeature.parameter>
53           <UML:Parameter isSpecification="false" visibility="private" xmi.id="n7GKuy9LN9fK" value="" type="dYy4jCaAkpGB" name="runDir" />
54          </UML:BehavioralFeature.parameter>
55         </UML:Operation>
56        </UML:Classifier.feature>
57       </UML:Class>
58       <UML:Class isSpecification="false" isLeaf="false" visibility="public" namespace="Logical View" xmi.id="ZEsHfPFxkUD5" isRoot="false" isAbstract="false" name="Jumpgate" >
59        <UML:Classifier.feature>
60         <UML:Operation isSpecification="false" isLeaf="false" visibility="public" xmi.id="crYTwksc84xx" isRoot="false" isAbstract="false" isQuery="false" name="rsync" />
61        </UML:Classifier.feature>
62       </UML:Class>
63       <UML:Class isSpecification="false" isLeaf="false" visibility="public" namespace="Logical View" xmi.id="fOCNrWNOlFdQ" isRoot="false" isAbstract="false" name="Cellcenter" >
64        <UML:Classifier.feature>
65         <UML:Operation isSpecification="false" isLeaf="false" visibility="public" xmi.id="bKJKYukBj6Uz" isRoot="false" isAbstract="false" isQuery="false" name="configPipeline" />
66         <UML:Operation isSpecification="false" isLeaf="false" visibility="public" xmi.id="dtnBd3KDtsgp" isRoot="false" isAbstract="false" isQuery="false" name="runPipeline" />
67        </UML:Classifier.feature>
68       </UML:Class>
69       <UML:Association isSpecification="false" visibility="public" namespace="Logical View" xmi.id="YzXPgsx8JY4f" name="" >
70        <UML:Association.connection>
71         <UML:AssociationEnd isSpecification="false" visibility="public" changeability="changeable" isNavigable="false" xmi.id="Xd2ysTXicS6i" aggregation="none" type="wDCVwIFrhMaS" name="" />
72         <UML:AssociationEnd isSpecification="false" visibility="public" changeability="changeable" isNavigable="true" xmi.id="iqOSoVoV96r4" aggregation="none" type="aary2tTYpejI" name="" />
73        </UML:Association.connection>
74       </UML:Association>
75      </UML:Namespace.ownedElement>
76      <XMI.extension xmi.extender="umbrello" >
77       <diagrams>
78        <diagram snapgrid="0" showattsig="1" fillcolor="#ffffc0" linewidth="0" zoom="100" showgrid="0" showopsig="1" usefillcolor="1" snapx="10" canvaswidth="908" snapy="10" showatts="1" xmi.id="qsXVOiQh2k6g" documentation="" type="1" showops="1" showpackage="0" name="class diagram" localid="" showstereotype="0" showscope="1" snapcsgrid="0" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="#ff0000" canvasheight="598" >
79         <widgets/>
80         <messages/>
81         <associations/>
82        </diagram>
83        <diagram snapgrid="1" showattsig="1" fillcolor="#ffffc0" linewidth="0" zoom="100" showgrid="1" showopsig="1" usefillcolor="1" snapx="10" canvaswidth="908" snapy="10" showatts="1" xmi.id="ngoLeq2pOCZE" documentation="" type="3" showops="1" showpackage="0" name="Automation Messages" localid="dqOLIZOnXkGB" showstereotype="0" showscope="1" snapcsgrid="0" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="#ff0000" canvasheight="598" >
84         <widgets>
85          <objectwidget usesdiagramfillcolor="0" width="112" x="150" fillcolor="#ffffc0" y="50" instancename="" linewidth="none" height="28" usefillcolor="1" isinstance="0" xmi.id="lZR99u8H0ec9" decon="0" localid="5MaOitMlK05R" multipleinstance="0" drawasactor="0" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,1,0,0,0" linecolor="#ff0000" />
86          <objectwidget usesdiagramfillcolor="0" width="64" x="300" fillcolor="#ffffc0" y="50" instancename="" linewidth="none" height="28" usefillcolor="1" isinstance="0" xmi.id="GkJy5VAr2ZyC" decon="0" localid="R6RQi1ZnL9A3" multipleinstance="0" drawasactor="0" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,1,0,0,0" linecolor="#ff0000" />
87          <objectwidget usesdiagramfillcolor="0" width="68" x="420" fillcolor="#ffffc0" y="50" instancename="" linewidth="none" height="28" usefillcolor="1" isinstance="0" xmi.id="0UoIUrhibyff" decon="0" localid="RnWUKUelY3BH" multipleinstance="0" drawasactor="0" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,1,0,0,0" linecolor="#ff0000" />
88          <objectwidget usesdiagramfillcolor="0" width="84" x="40" fillcolor="#ffffc0" y="50" instancename="" linewidth="none" height="28" usefillcolor="1" isinstance="0" xmi.id="ZEsHfPFxkUD5" decon="0" localid="X0MTdrbPt7CP" multipleinstance="0" drawasactor="0" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,1,0,0,0" linecolor="#ff0000" />
89          <objectwidget usesdiagramfillcolor="0" width="88" x="550" fillcolor="#ffffc0" y="50" instancename="" linewidth="none" height="28" usefillcolor="1" isinstance="0" xmi.id="fOCNrWNOlFdQ" decon="0" localid="dqOLIZOnXkGB" multipleinstance="0" drawasactor="0" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,1,0,0,0" linecolor="#ff0000" />
90          <notewidget usesdiagramfillcolor="1" width="84" x="610" fillcolor="none" y="320" linewidth="none" height="50" usefillcolor="1" isinstance="0" xmi.id="yQmtlfQN4OB7" text="Other Analysis" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" />
91         </widgets>
92         <messages>
93          <messagewidget usesdiagramfillcolor="1" width="124" x="207" fillcolor="none" y="122" operation="74kpdjSI8Fmc" linewidth="none" widgetbid="R6RQi1ZnL9A3" height="8" usefillcolor="1" seqnum="" textid="nCbzGolht3FI" widgetaid="5MaOitMlK05R" isinstance="0" xmi.id="74kpdjSI8Fmc" sequencemessagetype="1001" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" >
94           <floatingtext usesdiagramfillcolor="1" width="89" x="210" fillcolor="none" y="100" linewidth="none" posttext="" role="704" height="22" usefillcolor="1" pretext="" isinstance="0" xmi.id="nCbzGolht3FI" text=": startCopy()" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" />
95          </messagewidget>
96          <messagewidget usesdiagramfillcolor="1" width="124" x="207" fillcolor="none" y="156" operation="74kpdjSI8Fmc" linewidth="none" widgetbid="R6RQi1ZnL9A3" height="8" usefillcolor="1" seqnum="" textid="6DI3dhqqGq64" widgetaid="5MaOitMlK05R" isinstance="0" xmi.id="74kpdjSI8Fmc" sequencemessagetype="1001" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" >
97           <floatingtext usesdiagramfillcolor="1" width="89" x="210" fillcolor="none" y="130" linewidth="none" posttext="" role="704" height="22" usefillcolor="1" pretext="" isinstance="0" xmi.id="6DI3dhqqGq64" text=": startCopy()" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" />
98          </messagewidget>
99          <messagewidget usesdiagramfillcolor="1" width="124" x="207" fillcolor="none" y="211" operation="74kpdjSI8Fmc" linewidth="none" widgetbid="R6RQi1ZnL9A3" height="8" usefillcolor="1" seqnum="" textid="HQIrp1PvEiws" widgetaid="5MaOitMlK05R" isinstance="0" xmi.id="74kpdjSI8Fmc" sequencemessagetype="1001" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" >
100           <floatingtext usesdiagramfillcolor="1" width="89" x="230" fillcolor="none" y="190" linewidth="none" posttext="" role="704" height="22" usefillcolor="1" pretext="" isinstance="0" xmi.id="HQIrp1PvEiws" text=": startCopy()" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" />
101          </messagewidget>
102          <messagewidget usesdiagramfillcolor="1" width="124" x="207" fillcolor="none" y="253" operation="ZEGJnJU2LB4i" linewidth="none" widgetbid="R6RQi1ZnL9A3" height="8" usefillcolor="1" seqnum="" textid="fVIZsE2zucZA" widgetaid="5MaOitMlK05R" isinstance="0" xmi.id="ZEGJnJU2LB4i" sequencemessagetype="1001" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" >
103           <floatingtext usesdiagramfillcolor="1" width="243" x="210" fillcolor="none" y="230" linewidth="none" posttext="" role="704" height="22" usefillcolor="1" pretext="" isinstance="0" xmi.id="fVIZsE2zucZA" text=": sequencingFinished(runDir : string)" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" />
104          </messagewidget>
105          <messagewidget usesdiagramfillcolor="1" width="120" x="333" fillcolor="none" y="282" operation="t3UPqTGoZoip" linewidth="none" widgetbid="RnWUKUelY3BH" height="8" usefillcolor="1" seqnum="" textid="uyOuUAqAf6hV" widgetaid="R6RQi1ZnL9A3" isinstance="0" xmi.id="t3UPqTGoZoip" sequencemessagetype="1001" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" >
106           <floatingtext usesdiagramfillcolor="1" width="243" x="340" fillcolor="none" y="260" linewidth="none" posttext="" role="704" height="22" usefillcolor="1" pretext="" isinstance="0" xmi.id="uyOuUAqAf6hV" text=": sequencingFinished(runDir : string)" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" />
107          </messagewidget>
108          <messagewidget usesdiagramfillcolor="1" width="258" x="74" fillcolor="none" y="243" operation="crYTwksc84xx" linewidth="none" widgetbid="X0MTdrbPt7CP" height="32" usefillcolor="1" seqnum="" textid="R4DtGIV3Lxs4" widgetaid="R6RQi1ZnL9A3" isinstance="0" xmi.id="crYTwksc84xx" sequencemessagetype="1000" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" >
109           <floatingtext usesdiagramfillcolor="1" width="61" x="80" fillcolor="none" y="220" linewidth="none" posttext="" role="704" height="22" usefillcolor="1" pretext="" isinstance="0" xmi.id="R4DtGIV3Lxs4" text=": rsync()" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" />
110          </messagewidget>
111          <messagewidget usesdiagramfillcolor="1" width="138" x="455" fillcolor="none" y="302" operation="bKJKYukBj6Uz" linewidth="none" widgetbid="dqOLIZOnXkGB" height="8" usefillcolor="1" seqnum="" textid="jD2f9bGadRRu" widgetaid="RnWUKUelY3BH" isinstance="0" xmi.id="bKJKYukBj6Uz" sequencemessagetype="1001" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" >
112           <floatingtext usesdiagramfillcolor="1" width="118" x="460" fillcolor="none" y="280" linewidth="none" posttext="" role="704" height="22" usefillcolor="1" pretext="" isinstance="0" xmi.id="jD2f9bGadRRu" text=": configPipeline()" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" />
113          </messagewidget>
114          <messagewidget usesdiagramfillcolor="1" width="138" x="455" fillcolor="none" y="330" operation="dtnBd3KDtsgp" linewidth="none" widgetbid="dqOLIZOnXkGB" height="8" usefillcolor="1" seqnum="" textid="oy8nMfs4rsj0" widgetaid="RnWUKUelY3BH" isinstance="0" xmi.id="dtnBd3KDtsgp" sequencemessagetype="1001" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" >
115           <floatingtext usesdiagramfillcolor="1" width="99" x="470" fillcolor="none" y="310" linewidth="none" posttext="" role="704" height="22" usefillcolor="1" pretext="" isinstance="0" xmi.id="oy8nMfs4rsj0" text=": runPipeline()" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" />
116          </messagewidget>
117          <messagewidget usesdiagramfillcolor="1" width="258" x="74" fillcolor="none" y="145" operation="crYTwksc84xx" linewidth="none" widgetbid="X0MTdrbPt7CP" height="32" usefillcolor="1" seqnum="" textid="VoaFYvDhgi96" widgetaid="R6RQi1ZnL9A3" isinstance="0" xmi.id="crYTwksc84xx" sequencemessagetype="1000" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" >
118           <floatingtext usesdiagramfillcolor="1" width="61" x="80" fillcolor="none" y="120" linewidth="none" posttext="" role="704" height="22" usefillcolor="1" pretext="" isinstance="0" xmi.id="VoaFYvDhgi96" text=": rsync()" usesdiagramusefillcolor="1" font="Sans Serif,8,-1,5,50,0,0,0,0,0" linecolor="none" />
119          </messagewidget>
120         </messages>
121         <associations/>
122        </diagram>
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