| Previous changeset 7:33899d82fbc1 (2014-01-27) Next changeset 9:c317e0f939df (2014-02-07) |
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Commit message:
new option in file splitter; small fix in xtandem form |
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modified:
MassComb.jar masscomb_dbsearch_xtandem.xml masscomb_file_splitter.xml |
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| diff -r 33899d82fbc1 -r 153e9eb5f2ff MassComb.jar |
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| Binary file MassComb.jar has changed |
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| diff -r 33899d82fbc1 -r 153e9eb5f2ff masscomb_dbsearch_xtandem.xml --- a/masscomb_dbsearch_xtandem.xml Mon Jan 27 09:47:22 2014 +0100 +++ b/masscomb_dbsearch_xtandem.xml Fri Jan 31 12:06:57 2014 +0100 |
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| @@ -197,6 +197,9 @@ help="Max E-Value of a 'refine based' hit to be reported. Notice that the default value here is stricter than the same parameter for 'non-refine based' identifications above. "/> </when> + + <when value="no"> + </when> </conditional> <param name="reverse_scoring" type="select" label="Scoring, include reverse" help=" Use the X! Tandem protein sequence reverse method (sequences are reversed in memory and searched again, the tag ':reversed' is added to the protein description)."> <option value="yes">Yes</option> |
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| diff -r 33899d82fbc1 -r 153e9eb5f2ff masscomb_file_splitter.xml --- a/masscomb_file_splitter.xml Mon Jan 27 09:47:22 2014 +0100 +++ b/masscomb_file_splitter.xml Fri Jan 31 12:06:57 2014 +0100 |
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| @@ -18,9 +18,11 @@ <param name="splitExpression" type="select" label="(regular)Expression to split on" help=""> <option value="^>.+">line start with >alphanumeric (^>.+)</option> + <option value=".*<peak_listSLASHW+.*">APML peak_list tag (.*<peak_list\W+.*)</option> </param> <param name="nameExpression" type="select" label="(regular)Expression for file name" help=""> <option value="SLASHw+">alphanumeric part (\w)</option> + <option value="SLASHw+SLASH.raw">APML peak_list raw source file name (\w+\.raw)</option> </param> <param name="extension" type="text" size="30" label="File extension for the 'sub-files'" value=".txt" help=""/> @@ -34,6 +36,13 @@ </test> </tests> <help> - +This tool splits files of mainly custom formats. The lists of "Expression to split on" and +"Expression for file name" are populated based on feedback from users. Users don't need +to learn the regular expressions but can select options based on descriptions. +A free input text box for the expressions is not supported for a number of reasons, +one of them being the performance impact small errors could have. +<!-- furthermore galaxy is not escaping all special characters correctly, so + having a text input box where advanced users can type in their expressions is + not supported. --> </help> </tool> |