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comparison macros.xml @ 2:74cb429038c1 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
author iuc
date Sat, 13 Nov 2021 18:28:07 +0000
parents 1204e79d3a99
children
comparison
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1:1204e79d3a99 2:74cb429038c1
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&amp;4)</option> 36 <option value="34" selected="True">GC-content based normalization, WGS (3&amp;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 &quot;Read Count ~ GC-content&quot; 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 &quot;Read Count ~ GC-content&quot; 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="&quot;XX&quot; will exclude chr Y from the analysis. &quot;XY&quot; will not annotate one copy of chr X and Y as a loss."> 126 <param name="sex" type="select" label="Sample sex" help="&quot;XX&quot; will exclude chr Y from the analysis. &quot;XY&quot; 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 &quot;Yes&quot; 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 &quot;Yes&quot; if you want an additional output in BedGraph format for the UCSC genome browser." />