Mercurial > repos > iuc > control_freec
comparison macros.xml @ 1:1204e79d3a99 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
|---|---|
| date | Tue, 31 Aug 2021 08:10:37 +0000 |
| parents | 5330cf818142 |
| children | 74cb429038c1 |
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| 0:5330cf818142 | 1:1204e79d3a99 |
|---|---|
| 1 <macros> | 1 <macros> |
| 2 <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> | 2 <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token> |
| 3 <token name="@TOOL_VERSION@">11.6</token> | 3 <token name="@TOOL_VERSION@">11.6</token> |
| 4 <xml name="reference_interface"> | 4 <xml name="reference_interface"> |
| 5 <conditional name="reference_source"> | 5 <conditional name="reference_source"> |
| 6 <param name="ref_selector" type="select" label="Choose the source for the reference genome"> | 6 <param name="ref_selector" type="select" label="Choose the source for the reference genome"> |
| 7 <option value="cached">Locally cached</option> | 7 <option value="cached">Locally cached</option> |
| 38 <param name="readCountThreshold" type="integer" label="Threshold on the minimal number of reads per window" value="10" help="Threshold on the minimal number of reads per window in the control sample. Useful for exome-seq or targeted sequencing data. Default: 10 recommended value >=50 for for exome data." /> | 38 <param name="readCountThreshold" type="integer" label="Threshold on the minimal number of reads per window" value="10" help="Threshold on the minimal number of reads per window in the control sample. Useful for exome-seq or targeted sequencing data. Default: 10 recommended value >=50 for for exome data." /> |
| 39 <section name="window_section" title="Select window size" expanded="true"> | 39 <section name="window_section" title="Select window size" expanded="true"> |
| 40 <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"" /> | 40 <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"" /> |
| 41 <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" /> | 41 <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" /> |
| 42 </section> | 42 </section> |
| 43 <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." /> | |
| 44 <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" /> | |
| 43 </xml> | 45 </xml> |
| 44 <xml name="WES"> | 46 <xml name="WES"> |
| 45 <param name="degree" type="select" label="Degree of polynomial" help=""> | 47 <param name="degree" type="select" label="Degree of polynomial" help=""> |
| 46 <option value="34">GC-content based normalization, WGS (3&4)</option> | 48 <option value="34">GC-content based normalization, WGS (3&4)</option> |
| 47 <option value="1" selected="True">control-read-count-based normalization, WES (1)</option> | 49 <option value="1" selected="True">control-read-count-based normalization, WES (1)</option> |
| 59 <param name="readCountThreshold" type="integer" label="Threshold on the minimal number of reads per window" value="50" help="Threshold on the minimal number of reads per window in the control sample. Useful for exome-seq or targeted sequencing data. Default: 10 recommended value >=50 for for exome data." /> | 61 <param name="readCountThreshold" type="integer" label="Threshold on the minimal number of reads per window" value="50" help="Threshold on the minimal number of reads per window in the control sample. Useful for exome-seq or targeted sequencing data. Default: 10 recommended value >=50 for for exome data." /> |
| 60 <section name="window_section" title="Select window size" expanded="false"> | 62 <section name="window_section" title="Select window size" expanded="false"> |
| 61 <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"" /> | 63 <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"" /> |
| 62 <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" /> | 64 <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" /> |
| 63 </section> | 65 </section> |
| 66 <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." /> | |
| 67 <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" /> | |
| 64 </xml> | 68 </xml> |
| 65 <xml name="other"> | 69 <xml name="other"> |
| 66 <param name="degree" type="select" label="Degree of polynomial" help=""> | 70 <param name="degree" type="select" label="Degree of polynomial" help=""> |
| 67 <option value="34" selected="True">GC-content based normalization, WGS (3&4)</option> | 71 <option value="34" selected="True">GC-content based normalization, WGS (3&4)</option> |
| 68 <option value="1">control-read-count-based normalization, WES (1)</option> | 72 <option value="1">control-read-count-based normalization, WES (1)</option> |
| 80 <param name="readCountThreshold" type="integer" label="Threshold on the minimal number of reads per window" value="10" help="Threshold on the minimal number of reads per window in the control sample. Useful for exome-seq or targeted sequencing data. Default: 10 recommended value >=50 for for exome data." /> | 84 <param name="readCountThreshold" type="integer" label="Threshold on the minimal number of reads per window" value="10" help="Threshold on the minimal number of reads per window in the control sample. Useful for exome-seq or targeted sequencing data. Default: 10 recommended value >=50 for for exome data." /> |
| 81 <section name="window_section" title="Select window size" expanded="true"> | 85 <section name="window_section" title="Select window size" expanded="true"> |
| 82 <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"" /> | 86 <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"" /> |
| 83 <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" /> | 87 <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" /> |
| 84 </section> | 88 </section> |
| 89 <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." /> | |
| 90 <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" /> | |
| 85 </xml> | 91 </xml> |
| 86 <xml name="shared"> | 92 <xml name="shared"> |
| 87 <!-- general parameters --> | 93 <!-- general parameters --> |
| 88 <param name="breakPointThreshold" type="float" label="Segmentation of normalized profiles (break point)" value="0.8" help="Positive value of threshold for segmentation of normalized profiles. Use something like 0.6 to get more segments (and thus more predicted CNVs)." /> | 94 <param name="breakPointThreshold" type="float" label="Segmentation of normalized profiles (break point)" value="0.8" help="Positive value of threshold for segmentation of normalized profiles. Use something like 0.6 to get more segments (and thus more predicted CNVs)." /> |
| 89 <param name="breakPointType" type="select" label="Desired behavior in the ambiguous regions"> | 95 <param name="breakPointType" type="select" label="Desired behavior in the ambiguous regions"> |
| 103 <option value="1" selected="True">with GC-content (1)</option> | 109 <option value="1" selected="True">with GC-content (1)</option> |
| 104 </param> | 110 </param> |
| 105 <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)" /> | 111 <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)" /> |
| 106 <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." /> | 112 <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." /> |
| 107 <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." /> | 113 <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." /> |
| 108 <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" /> | |
| 109 <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" /> | 114 <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" /> |
| 110 <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." /> | |
| 111 <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."> | 115 <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."> |
| 112 <option value="XY" selected="True">XY</option> | 116 <option value="XY" selected="True">XY</option> |
| 113 <option value="XX">XX</option> | 117 <option value="XX">XX</option> |
| 114 <option value="no value"></option> | 118 <option value="no value"></option> |
| 115 </param> | 119 </param> |