Mercurial > repos > galaxyp > openms_converttramltotsv

comparison readme.md @ 2:e66eba918cf0 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 50c26f7fbe8a2bd1347c860d7a62480865efc254
author galaxyp
date Thu, 27 Apr 2017 13:17:13 -0400
parents 2b952d3e8c58
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1:2b952d3e8c58 2:e66eba918cf0
100 #end if 100 #end if
101 101
102 [...] 102 [...]
103 ]]> 103 ]]>
104 ``` 104 ```
105
106 * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
107
108 ```
109 <command><![CDATA[
110
111 ## check input file type
112 #set $in_type = $param_in.ext
105 113
106 * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: 114 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
115 ln -s '$param_in' 'param_in.${in_type}' &&
116
117 IDFileConverter
118
119 #if $param_in:
120 -in 'param_in.${in_type}'
121 #end if
122
123 [...]
124 ]]>
125 ```
126
127 * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
107 128
108 <data name="param_out" metadata_source="param_in" auto_format="true"/> 129 - `<data name="param_out" auto_format="true"/>`
130 - `<data name="param_out" metadata_source="param_in" auto_format="true"/>`
109 131
110 * 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. 132 * 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.
111 133
112 ``` 134 ```
113 <tests> 135 <tests>