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comparison scatter.xml @ 1:86cd76c3eecf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
author iuc
date Fri, 29 Sep 2023 15:36:43 +0000
parents 8fe2b3b3b190
children a3422357dbfc
comparison
equal deleted inserted replaced
0:8fe2b3b3b190 1:86cd76c3eecf
2 <description>Plot bin-level log2 coverages and segmentation calls together</description> 2 <description>Plot bin-level log2 coverages and segmentation calls together</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
7 <expand macro="creators"/>
7 <expand macro="requirements"/> 8 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_cnr_file' ./tumor.cnr && 10 ln -s '$input_cnr_file' ./tumor.cnr &&
10 #if $advanced_settings.segment 11 #if $advanced_settings.segment
11 ln -s '$advanced_settings.segment' ./segment.cns && 12 ln -s '$advanced_settings.segment' ./segment.cns &&
16 #if $advanced_settings.additional_SNP_allelic_process.vcf 17 #if $advanced_settings.additional_SNP_allelic_process.vcf
17 ln -s '$advanced_settings.additional_SNP_allelic_process.vcf' ./vcf_file.vcf && 18 ln -s '$advanced_settings.additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
18 #end if 19 #end if
19 cnvkit.py scatter 20 cnvkit.py scatter
20 ./tumor.cnr 21 ./tumor.cnr
21 --output sample-scatter.png 22 --output sample-scatter.pdf
22 #if $advanced_settings.segment 23 #if $advanced_settings.segment
23 --segment ./segment.cns 24 --segment ./segment.cns
24 #end if 25 #end if
25 #if $advanced_settings.chromosome 26 #if $advanced_settings.chromosome
26 --chromosome '$advanced_settings.chromosome' 27 --chromosome '$advanced_settings.chromosome'
69 #if str($advanced_settings.additional_SNP_allelic_process.zygosity_freq) 70 #if str($advanced_settings.additional_SNP_allelic_process.zygosity_freq)
70 --zygosity-freq $advanced_settings.additional_SNP_allelic_process.zygosity_freq 71 --zygosity-freq $advanced_settings.additional_SNP_allelic_process.zygosity_freq
71 #end if 72 #end if
72 ]]></command> 73 ]]></command>
73 <inputs> 74 <inputs>
74 <param name="input_cnr_file" type="data" format="tabular" label="cnn file" help="" /> 75 <param name="input_cnr_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="" />
75 <section name="advanced_settings" title="Advanced settings" expanded="false"> 76 <section name="advanced_settings" title="Advanced settings" expanded="false">
76 <expand macro="scatter_optional" /> 77 <expand macro="scatter_optional" />
77 <section name="plot_aesthetics" title="Plot aesthetics" expanded="false"> 78 <section name="plot_aesthetics" title="Plot aesthetics" expanded="false">
78 <expand macro="scatter_plot" /> 79 <expand macro="scatter_plot" />
79 </section> 80 </section>
81 <expand macro="additionally_SNP_process" /> 82 <expand macro="additionally_SNP_process" />
82 </section> 83 </section>
83 </section> 84 </section>
84 </inputs> 85 </inputs>
85 <outputs> 86 <outputs>
86 <data name="out_scatter_file" format="png" label="${tool.name} on ${on_string}: diagram pdf file" from_work_dir="sample-scatter.png" /> 87 <data name="out_scatter_file" format="pdf" label="${tool.name} on ${on_string}: Sample Scatter pdf file" from_work_dir="sample-scatter.pdf" />
87 </outputs> 88 </outputs>
88 <tests> 89 <tests>
89 <test expect_num_outputs="1"> 90 <test expect_num_outputs="1">
90 <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" /> 91 <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" />
91 <param name="zygosity_freq" value="0.25" /> 92 <param name="zygosity_freq" value="0.25" />
92 <param name="by_bin" value="1" /> 93 <param name="by_bin" value="1" />
93 <output name="out_scatter_file" file="sample-scatter.png" ftype="png" compare="sim_size"> 94 <output name="out_scatter_file" file="sample-scatter.pdf" ftype="pdf" compare="sim_size">
94 <assert_contents><has_size value="12000" delta="5000" /></assert_contents> 95 <assert_contents><has_size value="12000" delta="5000" /></assert_contents>
95 </output> 96 </output>
96 </test> 97 </test>
97 </tests> 98 </tests>
98 <help><![CDATA[ 99 <help><![CDATA[