Mercurial > repos > iuc > control_freec
diff macros.xml @ 1:2c6349fb175c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
| author | iuc |
|---|---|
| date | Tue, 18 Aug 2020 08:52:45 -0400 |
| parents | e46944a59b31 |
| children | f923c54a17ee |
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--- a/macros.xml Thu Aug 13 09:50:35 2020 -0400 +++ b/macros.xml Tue Aug 18 08:52:45 2020 -0400 @@ -1,5 +1,5 @@ <macros> - <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> + <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token> <token name="@TOOL_VERSION@">11.6</token> <xml name="reference_interface"> <conditional name="reference_source"> @@ -40,6 +40,8 @@ <param name="window" type="integer" value="50000" label="Explicit window size" help="Higher priority than coefficientOfVariation. Ex: for whole genome sequencing: "50000"; for whole exome sequencing: "0"" /> <param name="step" type="integer" value="10000" label="Step" help="Used only when "window" is specified. Do not use for exome sequencing (instead set "0"). Ex: 10000" /> </section> + <param name="printNA" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Print NA to avoid "-1"" help="Set "No" to avoid printing "-1" to the _ratio.txt files. Useful for exome-seq or targeted sequencing data." /> + <param name="noisyData" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Noisy Data" help="Set "Yes" for target resequencing data (e.g., exome-seq) to avoid false positive predictions due to non-uniform capture" /> </xml> <xml name="WES"> <param name="degree" type="select" label="Degree of polynomial" help=""> @@ -61,6 +63,8 @@ <param name="window" type="integer" value="0" label="Explicit window size" help="Higher priority than coefficientOfVariation. Ex: for whole genome sequencing: "50000"; for whole exome sequencing: "0"" /> <param name="step" type="integer" value="0" label="Step" help="Used only when "window" is specified. Do not use for exome sequencing (instead set "0"). Ex: 10000" /> </section> + <param name="printNA" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Print NA to avoid "-1"" help="Set "No" to avoid printing "-1" to the _ratio.txt files. Useful for exome-seq or targeted sequencing data." /> + <param name="noisyData" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Noisy Data" help="Set "Yes" for target resequencing data (e.g., exome-seq) to avoid false positive predictions due to non-uniform capture" /> </xml> <xml name="other"> <param name="degree" type="select" label="Degree of polynomial" help=""> @@ -82,6 +86,8 @@ <param name="window" type="integer" value="50000" label="Explicit window size" help="Higher priority than coefficientOfVariation. Ex: for whole genome sequencing: "50000"; for whole exome sequencing: "0"" /> <param name="step" type="integer" value="10000" label="Step" help="Used only when "window" is specified. Do not use for exome sequencing (instead set "0"). Ex: 10000" /> </section> + <param name="printNA" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Print NA to avoid "-1"" help="Set "No" to avoid printing "-1" to the _ratio.txt files. Useful for exome-seq or targeted sequencing data." /> + <param name="noisyData" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Noisy Data" help="Set "Yes" for target resequencing data (e.g., exome-seq) to avoid false positive predictions due to non-uniform capture" /> </xml> <xml name="shared"> <!-- general parameters --> @@ -105,9 +111,7 @@ <param name="minMappabilityPerWindow" type="float" label="Minimal mappability per window" value="0.85" min="0" max="1" help="Only windows with fraction of mappable positions higher than or equal to this threshold will be considered (if "gemMappabilityFile" is not provided, one uses the percentage of non-N letters per window)" /> <param name="minExpectedGC" type="float" label="Minimal expected value of the GC-content" value="0.35" min="0" max="1" help="Minimal expected value of the GC-content for the prior evaluation of "Read Count ~ GC-content" dependency. Change only if you run Control-FREEC on a bacterial genome." /> <param name="maxExpectedGC" type="float" label="Maximal expected value of the GC-content" value="0.55" min="0" max="1" help="Maximal expected value of the GC-content for the prior evaluation of "Read Count ~ GC-content" dependency. Change only if you run Control-FREEC on a bacterial genome." /> - <param name="noisyData" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Noisy Data" help="Set "Yes" for target resequencing data (e.g., exome-seq) to avoid false positive predictions due to non-uniform capture" /> <param name="ploidy" type="text" value="2" label="Genome ploidy" help="In case of doubt, you can set different values and Control-FREEC will select the one that explains most observed CNAs. Ex: 2 or 2,3,4" /> - <param name="printNA" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Print NA to avoid "-1"" help="Set "No" to avoid printing "-1" to the _ratio.txt files. Useful for exome-seq or targeted sequencing data." /> <param name="sex" type="select" label="Sample sex" help=""XX" will exclude chr Y from the analysis. "XY" will not annotate one copy of chr X and Y as a loss."> <option value="XY" selected="True">XY</option> <option value="XX">XX</option>