Mercurial > repos > iuc > control_freec
comparison macros.xml @ 2:f923c54a17ee draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
author | iuc |
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date | Sat, 13 Nov 2021 18:28:40 +0000 |
parents | 2c6349fb175c |
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1:2c6349fb175c | 2:f923c54a17ee |
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1 <macros> | 1 <macros> |
2 <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token> | 2 <token name="@VERSION_SUFFIX@">2</token> |
3 <token name="@TOOL_VERSION@">11.6</token> | 3 <token name="@TOOL_VERSION@">11.6</token> |
4 <xml name="requirements"> | |
5 <requirements> | |
6 <requirement type="package" version="5.0.1">gawk</requirement> | |
7 <requirement type="package" version="@TOOL_VERSION@">control-freec</requirement> | |
8 </requirements> | |
9 </xml> | |
4 <xml name="reference_interface"> | 10 <xml name="reference_interface"> |
5 <conditional name="reference_source"> | 11 <conditional name="reference_source"> |
6 <param name="ref_selector" type="select" label="Choose the source for the reference genome"> | 12 <param name="ref_selector" type="select" label="Choose the source for the reference genome"> |
7 <option value="cached">Locally cached</option> | 13 <option value="cached">Locally cached</option> |
8 <option value="history">History</option> | 14 <option value="history">History</option> |
17 </when> | 23 </when> |
18 <when value="history"> | 24 <when value="history"> |
19 <param argument="--ref" type="data" format="fasta" label="Reference" help="Reference sequence" /> | 25 <param argument="--ref" type="data" format="fasta" label="Reference" help="Reference sequence" /> |
20 </when> | 26 </when> |
21 </conditional> | 27 </conditional> |
28 </xml> | |
29 <xml name="xrefs"> | |
30 <xrefs> | |
31 <xref type="bio.tools">freec</xref> | |
32 </xrefs> | |
22 </xml> | 33 </xml> |
23 <xml name="WGS"> | 34 <xml name="WGS"> |
24 <param name="degree" type="select" label="Degree of polynomial" help=""> | 35 <param name="degree" type="select" label="Degree of polynomial" help=""> |
25 <option value="34" selected="True">GC-content based normalization, WGS (3&4)</option> | 36 <option value="34" selected="True">GC-content based normalization, WGS (3&4)</option> |
26 <option value="1">control-read-count-based normalization, WES (1)</option> | 37 <option value="1">control-read-count-based normalization, WES (1)</option> |
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." /> | 124 <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." /> |
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" /> | 125 <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" /> |
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."> | 126 <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."> |
116 <option value="XY" selected="True">XY</option> | 127 <option value="XY" selected="True">XY</option> |
117 <option value="XX">XX</option> | 128 <option value="XX">XX</option> |
118 <option value="no value"></option> | 129 <option value="no value">Do not expecify sex</option> |
119 </param> | 130 </param> |
120 <param name="telocentromeric" type="integer" value="50000" label="Length of pre-telomeric and pre-centromeric regions" help="Control-FREEC will not output small CNAs and LOH found within these regions (they are likely to be false because of mappability/genome assembly issues). 50000 is OK for human/mouse genomes. Use smaller values for yeasts and flies. Do not set anything for exome-seq data." /> | 131 <param name="telocentromeric" type="integer" value="50000" label="Length of pre-telomeric and pre-centromeric regions" help="Control-FREEC will not output small CNAs and LOH found within these regions (they are likely to be false because of mappability/genome assembly issues). 50000 is OK for human/mouse genomes. Use smaller values for yeasts and flies. Do not set anything for exome-seq data." /> |
121 <!-- uniqueMatch if true -> gemMappabilityFile is needed--> | 132 <!-- uniqueMatch if true -> gemMappabilityFile is needed--> |
122 <!-- BAF parameters --> | 133 <!-- BAF parameters --> |
123 <!-- makePileup: path to a BED or VCF file with SNP positions --> | 134 <!-- makePileup: path to a BED or VCF file with SNP positions --> |
137 </xml> | 148 </xml> |
138 <xml name="input_control_sample"> | 149 <xml name="input_control_sample"> |
139 <param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample file" help="Sample file in .BAM format." /> | 150 <param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample file" help="Sample file in .BAM format." /> |
140 <param name="input_control_file" type="data" format="bam" multiple="false" label="Control file" help="Control file in .BAM format." /> | 151 <param name="input_control_file" type="data" format="bam" multiple="false" label="Control file" help="Control file in .BAM format." /> |
141 </xml> | 152 </xml> |
153 <xml name="input_control_sample_wgs"> | |
154 <param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample file" help="Sample file in .BAM format." /> | |
155 <param name="input_control_file" type="data" format="bam" multiple="false" optional="true" label="Control file" help="Control file in .BAM format." /> | |
156 </xml> | |
142 <xml name="wes_input_files"> | 157 <xml name="wes_input_files"> |
143 <expand macro="input_control_sample" /> | 158 <expand macro="input_control_sample" /> |
144 <param name="input_capture_file" optional="true" type="data" format="bed" multiple="false" label="BED file with capture regions" help="Capture regions in .BED format." /> | 159 <param name="input_capture_file" optional="true" type="data" format="bed" multiple="false" label="BED file with capture regions" help="Capture regions in .BED format." /> |
145 <expand macro="mateOrientation_selector" /> | 160 <expand macro="mateOrientation_selector" /> |
146 </xml> | 161 </xml> |
147 <xml name="def_input_files"> | 162 <xml name="wgs_input_files"> |
148 <expand macro="input_control_sample" /> | 163 <expand macro="input_control_sample_wgs" /> |
149 <expand macro="mateOrientation_selector" /> | 164 <expand macro="mateOrientation_selector" /> |
150 </xml> | 165 </xml> |
151 <xml name="output_section"> | 166 <xml name="output_section"> |
152 <section name="output_section" title="Outputs" expanded="false"> | 167 <section name="output_section" title="Outputs" expanded="false"> |
153 <param name="BedGraphOutput" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="BedGraph Output for UCSC genome browser" help="Set "Yes" if you want an additional output in BedGraph format for the UCSC genome browser." /> | 168 <param name="BedGraphOutput" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="BedGraph Output for UCSC genome browser" help="Set "Yes" if you want an additional output in BedGraph format for the UCSC genome browser." /> |