Mercurial > repos > pieterlukasse > prims_proteomics
changeset 6:d1edc7971d48
fixes in tool forms (<when> tags)
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Fri, 31 Jan 2014 12:11:34 +0100 |
| parents | 5d99c9d0615d |
| children | 6a95bdfbe36d |
| files | Csv2Apml.jar MsFilt.jar NapQ.jar PRIMS.jar ProgenesisConv.jar Quantifere.jar Quantiline.jar SedMat_cli.jar isofix.xml napq.xml progenesisconverter.xml quantifere.xml sedmat.xml |
| diffstat | 13 files changed, 16 insertions(+), 2 deletions(-) [+] |
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--- a/isofix.xml Mon Jan 27 12:11:29 2014 +0100 +++ b/isofix.xml Fri Jan 31 12:11:34 2014 +0100 @@ -33,6 +33,8 @@ <when value="Yes"> <param name="fastaFile" type="data" format="fasta" label="Protein sequences (fasta file)"/> </when> + <when value="No"> + </when> </conditional> </inputs>
--- a/napq.xml Mon Jan 27 12:11:29 2014 +0100 +++ b/napq.xml Fri Jan 31 12:11:34 2014 +0100 @@ -8,9 +8,9 @@ <command interpreter="java -jar "> NapQ.jar -identificationsConfigFile $identificationsConfigFile - -namingConventionCodesForSamples $namingConventionCodesForSamples + -namingConventionCodesForSamples "$namingConventionCodesForSamples" #if $is2D_LC_MS.fractions == True - -namingConventionCodesForFractions $is2D_LC_MS.namingConventionCodesForFractions + -namingConventionCodesForFractions "$is2D_LC_MS.namingConventionCodesForFractions" #end if -outputApml $outputApml -outputTsv $outputTsv @@ -43,6 +43,8 @@ and that stand for a fraction code. E.g. '_F1,_F2,_F3,etc.' Use this to avoid that each (fraction) file is seen as a separate run."/> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b --> </when> + <when value="No"> + </when> </conditional> </inputs>
--- a/progenesisconverter.xml Mon Jan 27 12:11:29 2014 +0100 +++ b/progenesisconverter.xml Fri Jan 31 12:11:34 2014 +0100 @@ -30,6 +30,8 @@ label="Column name" help="Name of the column containing the scoring scheme name" /> </when> + <when value="No"> + </when> </conditional> <conditional name="statisticalMeasure"> @@ -41,6 +43,8 @@ label="Column name" help="Name of the column containing the statistical measure" /> </when> + <when value="No"> + </when> </conditional> </inputs>
--- a/quantifere.xml Mon Jan 27 12:11:29 2014 +0100 +++ b/quantifere.xml Fri Jan 31 12:11:34 2014 +0100 @@ -57,6 +57,8 @@ in different fractions can be merged together. Otherwise each (fraction) file is seen as a separate sample."/> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b --> </when> + <when value="No"> + </when> </conditional> <param name="statisticalMeasuresConfig" type="text" area="true" size="6x70" label="Statistical measures configuration"
--- a/sedmat.xml Mon Jan 27 12:11:29 2014 +0100 +++ b/sedmat.xml Fri Jan 31 12:11:34 2014 +0100 @@ -89,6 +89,8 @@ <when value="Yes"> <param name="namingConventionCodesForMatching" type="text" size="100" value="" label="List of codes in naming convention" help="Add the CSV list of codes that occur in the file names and that link them together. E.g. '_F1,_F2,_F3,etc.'"/> </when> + <when value="No"> + </when> </conditional> <param name="chargeStatesToGenerate" type="select" display="checkboxes" multiple="true" label="Generate extra charge states" help="The selected charge states will be generated for each MS2 feature "> @@ -110,6 +112,8 @@ <param name="rtEnd" optional="false" type="integer" size="10" value="20" label="Set rention time end (minutes) " /> <param name="filterSourceName" type="text" size="100" value="" label="Restrict matching to a specific subset of the files " help="Part of a file name that occurs in both a ms1 and ms2 file (e.g. 'RibO_1_msE1')"/> </when> + <when value="No"> + </when> </conditional> </inputs>