Mercurial > repos > galaxyp > msconvert
comparison msconvert3.xml @ 3:7e41529ee90c
added repo and tool dependencies
| author | galaxyp |
|---|---|
| date | Thu, 20 Jun 2013 16:08:23 -0400 |
| parents | 861e3f0c2bb6 |
| children | 001e77708ec9 |
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| 2:50e30fb68be2 | 3:7e41529ee90c |
|---|---|
| 2 <!-- BEGIN_VERSION_DEFAULT --> | 2 <!-- BEGIN_VERSION_DEFAULT --> |
| 3 <description>Convert and filter a mass spec peak list</description> | 3 <description>Convert and filter a mass spec peak list</description> |
| 4 <!-- END_VERSION_DEFAULT --> | 4 <!-- END_VERSION_DEFAULT --> |
| 5 | 5 |
| 6 <command interpreter="python"> | 6 <command interpreter="python"> |
| 7 #set $ext = $input.ext | |
| 8 #if $ext.startswith("m:") | |
| 9 #set $ext = $ext[len("m:"):] | |
| 10 #end if | |
| 7 msconvert_wrapper.py | 11 msconvert_wrapper.py |
| 8 --input=${input} | 12 --input=${input} |
| 9 #if hasattr($input, 'display_name') | 13 #if hasattr($input, 'display_name') |
| 10 --input_name='${input.display_name}' | 14 --input_name='${input.display_name}' |
| 11 #end if | 15 #end if |
| 12 --output=${output} | 16 --output=${output} |
| 13 ## BEGIN_VERSION_DEFAULT | 17 ## BEGIN_VERSION_DEFAULT |
| 14 --fromextension=${input.ext} | 18 --fromextension=$ext |
| 15 ## END_VERSION_DEFAULT | 19 ## END_VERSION_DEFAULT |
| 16 | 20 |
| 17 | 21 |
| 18 --toextension=${output_type} | 22 --toextension=${output_type} |
| 19 | 23 |