Mercurial > repos > galaxyp > openms_featurelinkerlabeled
changeset 2:a07f3900f271 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 50c26f7fbe8a2bd1347c860d7a62480865efc254
| author | galaxyp |
|---|---|
| date | Thu, 27 Apr 2017 13:20:50 -0400 |
| parents | 77f29f5244d9 |
| children | 1fc3597af7da |
| files | readme.md |
| diffstat | 1 files changed, 24 insertions(+), 2 deletions(-) [+] |
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--- a/readme.md Tue Apr 18 16:05:20 2017 -0400 +++ b/readme.md Thu Apr 27 13:20:50 2017 -0400 @@ -102,10 +102,32 @@ [...] ]]> ``` + + * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): + + ``` + <command><![CDATA[ + + ## check input file type + #set $in_type = $param_in.ext - * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: + ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files + ln -s '$param_in' 'param_in.${in_type}' && + + IDFileConverter + + #if $param_in: + -in 'param_in.${in_type}' + #end if + + [...] + ]]> + ``` + + * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.: - <data name="param_out" metadata_source="param_in" auto_format="true"/> + - `<data name="param_out" auto_format="true"/>` + - `<data name="param_out" metadata_source="param_in" auto_format="true"/>` * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files.