On 11/10/2012 12:05, Bas Jansen wrote:
Dear Alan,
Hello
PeptMoiety expects two files passed to it (when running it on the
command line), I would like to try the file option but will need the way
to go around this issue with input being a list of files so if you would
be willing to share that, that would be greatly appreciated.
Here is one possibility:
There is the option to pass a list of data. Each item in the list is
written into a temporary file and then another "index" file is created
that contains the paths to the temporary file. So, if you can pass the
contents of those files rather than the paths to them, then you can use
this mechanism.
I'm attaching a very simple example. The file list is available under
the Advanced tab of the tool service.
[snip]
Bas
Alan
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<mechanismXML><?xml version="1.0" encoding="UTF-8"?>
<localInvocation><shellPrefix>/bin/sh
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%%TARGET_NAME%%</linkCommand></localInvocation>
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<externaltoolid>f0e740ae-e60b-421b-9cab-287988d1dbca</externaltoolid>
<useCaseDescription>
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<tags />
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<queue__preferred />
<queue__deny />
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<entry>
<string>in1</string>
<de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
<tag>in1</tag>
<file>true</file>
<tempFile>false</tempFile>
<binary>false</binary>
<charsetName>MacRoman</charsetName>
<forceCopy>false</forceCopy>
<list>true</list>
<concatenate>false</concatenate>
<mime />
</de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
</entry>
</inputs>
<outputs />
<includeStdIn>false</includeStdIn>
<includeStdOut>true</includeStdOut>
<includeStdErr>true</includeStdErr>
<validReturnCodes>
<int>0</int>
</validReturnCodes>
</useCaseDescription>
<edited>false</edited>
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<backoffFactor>1.0</backoffFactor>
<initialDelay>1000</initialDelay>
<maxDelay>5000</maxDelay>
<maxRetries>0</maxRetries>
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encoding="xstream"><null xmlns=""
/></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port
name="in1" depth="1"
/></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions
/><datalinks><datalink><sink
type="processor"><processor>Tool</processor><port>in1</port></sink><source
type="dataflow"><port>Tool_in1</port></source></datalink><datalink><sink
type="dataflow"><port>Tool_STDOUT</port></sink><source
type="processor"><processor>Tool</processor><port>STDOUT</port></source></datalink></datalinks><annotations><annotation_chain
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<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean
class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
<text>This example workflow shows how a list of data items can be
written to temporary files and an index file created.</text>
</annotationBean>
<date>2012-10-11 11:48:09.862 UTC</date>
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<curationEventList />
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<identification>f41b5e1c-218a-4773-ab84-6f2e5d948cde</identification>
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<date>2012-10-11 11:41:28.922 UTC</date>
<creators />
<curationEventList />
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2
encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean
class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>6c71b9b7-8607-4170-8e40-e38580024964</identification>
</annotationBean>
<date>2012-10-11 11:48:18.656 UTC</date>
<creators />
<curationEventList />
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain
encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean
class="net.sf.taverna.t2.annotation.annotationbeans.Author">
<text>Alan R Williams</text>
</annotationBean>
<date>2012-10-11 11:47:06.838 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain
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<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean
class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
<text>Simple data list example</text>
</annotationBean>
<date>2012-10-11 11:47:14.438 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>------------------------------------------------------------------------------
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