How to run the new code/methods on a set of image files?

[rossmounce]

When I run

mvn clean install

I can see exciting new NeXML output for one file / set of tests, output to this path:

./ami-plugin/target/phylo/image/003.pbm.png/
├── edited.nexml.xml
└── edited.nwk
0 directories, 2 files

How can, or should I run these methods on a set of input files?
Previously I was running the below, but I have tried this and I don't get new style NeXML with cmphy namespace, edits and lookups:

#where ls.txt contains a list of input image files+paths to them, one per line
while read i ; do timeout 60s mvn exec:java  -Dexec.mainClass='org.xmlcml.ami2.plugins.phylotree.RunPhylo'  -Dexec.args=''"$i"' 50-output/'"$i"'' -e -X | tee $i.log ; done <ls.txt

I guess, I need to either amend RunPhylo, or exec a totally different java file?

[petermr]

This is run as a test and I need to customise it to run from the
commandline and choose the appropriate output directory.

On Mon, Aug 24, 2015 at 11:02 PM, Ross Mounce notifications@github.com
wrote:

When I run

mvn clean install

I can see exciting new NeXML output for one file / set of tests, output to
this path:

./ami-plugin/target/phylo/image/003.pbm.png/
├── edited.nexml.xml
└── edited.nwk
0 directories, 2 files

How can, or should I run these methods on a set of input files?
Previously I was running the below, but I have tried this and I don't get
new style NeXML with cmphy namespace, edits and lookups:

#where ls.txt contains a list of input image files+paths to them, one per line
while read i ; do timeout 60s mvn exec:java -Dexec.mainClass='org.xmlcml.ami2.plugins.phylotree.RunPhylo' -Dexec.args=''"$i"' 50-output/'"$i"'' -e -X | tee $i.log ; done <ls.txt

I guess, I need to either amend RunPhylo, or exec a totally different java
file?

—
Reply to this email directly or view it on GitHub
#53.

Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069

[rossmounce]

I will read up on XSLT in the mean time