Mercurial > repos > iuc > cnvkit_scatter

annotate scatter.xml @ 5:64960243c9e1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 12:04:46 +0000
parents 02446206f574
children
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ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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1 <tool id="cnvkit_scatter" name="CNVkit Scatter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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2 <description>Plot bin-level log2 coverages and segmentation calls together</description>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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3 <macros>
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4 <import>macros.xml</import>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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5 </macros>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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6 <expand macro="xrefs"/>
1
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7 <expand macro="creators"/>
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ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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10 ln -s '$input_cnr_file' ./tumor.cnr &&
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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11 #if $advanced_settings.segment
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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12 ln -s '$advanced_settings.segment' ./segment.cns &&
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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13 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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14 #if $advanced_settings.range_list
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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15 ln -s '$advanced_settings.range_list' ./list.bed &&
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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16 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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17 #if $advanced_settings.additional_SNP_allelic_process.vcf
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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18 ln -s '$advanced_settings.additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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19 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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20 cnvkit.py scatter
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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21 ./tumor.cnr
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22 --output sample-scatter.pdf
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23 #if $advanced_settings.segment
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24 --segment ./segment.cns
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25 #end if
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26 #if $advanced_settings.chromosome
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27 --chromosome '$advanced_settings.chromosome'
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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28 #end if
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29 #if $advanced_settings.gene
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30 --gene '$advanced_settings.gene'
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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31 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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32 #if $advanced_settings.range_list
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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33 --range-list ./list.bed
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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34 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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35 #if str($advanced_settings.width)
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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36 --width $advanced_settings.width
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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37 #end if
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38 #if $advanced_settings.plot_aesthetics.antitarget_marker
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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39 --antitarget-marker '$advanced_settings.plot_aesthetics.antitarget_marker'
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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40 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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41 $advanced_settings.plot_aesthetics.by_bin
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42 #if $advanced_settings.plot_aesthetics.segment_color
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43 --segment-color '$advanced_settings.plot_aesthetics.segment_color'
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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44 #end if
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45 #if $advanced_settings.plot_aesthetics.title
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46 --title '$advanced_settings.plot_aesthetics.title'
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47 #end if
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48 $advanced_settings.plot_aesthetics.trend
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49 #if str($advanced_settings.plot_aesthetics.y_max)
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50 --y-max $advanced_settings.plot_aesthetics.y_max
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51 #end if
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52 #if str($advanced_settings.plot_aesthetics.y_min)
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53 --y-min $advanced_settings.plot_aesthetics.y_min
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54 #end if
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55 #if str($advanced_settings.plot_aesthetics.fig_size)
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56 --fig-size $advanced_settings.plot_aesthetics.fig_size
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57 #end if
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58 #if $advanced_settings.additional_SNP_allelic_process.vcf
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59 --vcf ./vcf_file.vcf
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60 #end if
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61 #if $advanced_settings.additional_SNP_allelic_process.sample_id
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62 --sample-id '$advanced_settings.additional_SNP_allelic_process.sample_id'
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63 #end if
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64 #if $advanced_settings.additional_SNP_allelic_process.normal_id
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65 --normal-id '$advanced_settings.additional_SNP_allelic_process.normal_id'
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66 #end if
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67 #if str($advanced_settings.additional_SNP_allelic_process.min_variant_depth)
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68 --min-variant-depth $advanced_settings.additional_SNP_allelic_process.min_variant_depth
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69 #end if
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70 #if str($advanced_settings.additional_SNP_allelic_process.zygosity_freq)
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71 --zygosity-freq $advanced_settings.additional_SNP_allelic_process.zygosity_freq
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72 #end if
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73 ]]></command>
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74 <inputs>
5
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75 <param name="input_cnr_file" type="data" format="cnr" label="Bin-Level log2 Ratios/Coverages cnr file" help="" />
0
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76 <section name="advanced_settings" title="Advanced settings" expanded="false">
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77 <expand macro="scatter_optional" />
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78 <section name="plot_aesthetics" title="Plot aesthetics" expanded="false">
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79 <expand macro="scatter_plot" />
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80 </section>
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81 <section name="additional_SNP_allelic_process" title="Plot aesthetics" expanded="false">
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82 <expand macro="additionally_SNP_process" />
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83 </section>
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84 </section>
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85 </inputs>
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86 <outputs>
1
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87 <data name="out_scatter_file" format="pdf" label="${tool.name} on ${on_string}: Sample Scatter pdf file" from_work_dir="sample-scatter.pdf" />
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88 </outputs>
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89 <tests>
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90 <test expect_num_outputs="1">
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91 <param name="input_cnr_file" ftype="cnr" value="tumor.cnr" />
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92 <section name="advanced_settings">
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93 <section name="additional_SNP_allelic_process">
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94 <param name="zygosity_freq" value="0.25" />
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95 </section>
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96 <section name="plot_aesthetics">
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97 <param name="by_bin" value="1" />
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98 </section>
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99 </section>
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100 <output name="out_scatter_file" file="sample-scatter.pdf" ftype="pdf" compare="sim_size">
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101 <assert_contents><has_size value="12000" delta="5000" /></assert_contents>
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102 </output>
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103 </test>
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104 </tests>
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105 <help><![CDATA[
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106 Plot bin-level log2 coverages and segmentation calls together. Without any further arguments,
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107 this plots the genome-wide copy number in a form familiar to those who have used array CGH.
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108
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109 -----
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110
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111 **Bin-level log2 ratios (.cnr)**
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112
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113 Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.
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114
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115 .. csv-table::
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116 :header-rows: 0
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117
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118 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
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119 "start","Start position of the bin."
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120 "end","End position of the bin."
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121 "gene","Gene name(s) overlapping the bin (if applicable)."
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122 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
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123 "depth","Average read depth in the bin."
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124 "weight","Reliability weight of the bin (higher = more reliable)."
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125
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126 -----
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127
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128 **Segmented log2 ratios (.cns)**
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129
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130 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
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131
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132 .. csv-table::
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133 :header-rows: 0
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134
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135 "chromosome","start, end: Genomic coordinates of the segment"
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136 "gene","Gene(s) overlapping the segment."
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137 "log2","Mean log2 ratio of the segment."
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138 "probes","Mean log2 ratio of the segment."
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139 "depth","Average read depth."
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140 "weight","Reliability weight."
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141 "p_value","Statistical confidence (lower = more significant)."
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142
0
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143 ]]></help>
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144 <expand macro="citations" />
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145 </tool>