Mercurial > repos > iuc > cnvkit_scatter

annotate scatter.xml @ 0:ec9731970f8b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
author iuc
date Sun, 14 May 2023 20:10:25 +0000
parents
children 3323a7867128
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
3 <macros>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
4 <import>macros.xml</import>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
5 </macros>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
6 <expand macro="xrefs"/>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
9 ln -s '$input_cnr_file' ./tumor.cnr &&
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
10 #if $advanced_settings.segment
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
11 ln -s '$advanced_settings.segment' ./segment.cns &&
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
12 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
13 #if $advanced_settings.range_list
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
14 ln -s '$advanced_settings.range_list' ./list.bed &&
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
15 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
16 #if $advanced_settings.additional_SNP_allelic_process.vcf
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
17 ln -s '$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
iuc
parents:
diff changeset
18 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
19 cnvkit.py scatter
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
20 ./tumor.cnr
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
21 --output sample-scatter.png
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
22 #if $advanced_settings.segment
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
23 --segment ./segment.cns
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
24 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
25 #if $advanced_settings.chromosome
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
26 --chromosome '$advanced_settings.chromosome'
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
27 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
28 #if $advanced_settings.gene
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
29 --gene '$advanced_settings.gene'
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
30 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
31 #if $advanced_settings.range_list
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
32 --range-list ./list.bed
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
33 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
34 #if str($advanced_settings.width)
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
35 --width $advanced_settings.width
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
36 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
37 #if $advanced_settings.plot_aesthetics.antitarget_marker
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
38 --antitarget-marker '$advanced_settings.plot_aesthetics.antitarget_marker'
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
39 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
40 $advanced_settings.plot_aesthetics.by_bin
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
41 #if $advanced_settings.plot_aesthetics.segment_color
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
42 --segment-color '$advanced_settings.plot_aesthetics.segment_color'
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
43 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
44 #if $advanced_settings.plot_aesthetics.title
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
45 --title '$advanced_settings.plot_aesthetics.title'
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
46 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
47 $advanced_settings.plot_aesthetics.trend
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
48 #if str($advanced_settings.plot_aesthetics.y_max)
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
49 --y-max $advanced_settings.plot_aesthetics.y_max
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
50 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
51 #if str($advanced_settings.plot_aesthetics.y_min)
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
52 --y-min $advanced_settings.plot_aesthetics.y_min
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
53 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
54 #if str($advanced_settings.plot_aesthetics.fig_size)
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
55 --fig-size $advanced_settings.plot_aesthetics.fig_size
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
56 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
57 #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
iuc
parents:
diff changeset
58 --vcf ./vcf_file.vcf
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
59 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
60 #if $advanced_settings.additional_SNP_allelic_process.sample_id
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
61 --sample-id '$advanced_settings.additional_SNP_allelic_process.sample_id'
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
62 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
63 #if $advanced_settings.additional_SNP_allelic_process.normal_id
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
64 --normal-id '$advanced_settings.additional_SNP_allelic_process.normal_id'
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
65 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
66 #if str($advanced_settings.additional_SNP_allelic_process.min_variant_depth)
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
67 --min-variant-depth $advanced_settings.additional_SNP_allelic_process.min_variant_depth
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
68 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
69 #if str($advanced_settings.additional_SNP_allelic_process.zygosity_freq)
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
70 --zygosity-freq $advanced_settings.additional_SNP_allelic_process.zygosity_freq
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
71 #end if
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
72 ]]></command>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
73 <inputs>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
74 <param name="input_cnr_file" type="data" format="tabular" label="cnn file" help="" />
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
75 <section name="advanced_settings" title="Advanced settings" expanded="false">
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
76 <expand macro="scatter_optional" />
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
77 <section name="plot_aesthetics" title="Plot aesthetics" expanded="false">
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
78 <expand macro="scatter_plot" />
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
79 </section>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
80 <section name="additional_SNP_allelic_process" title="Plot aesthetics" expanded="false">
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
81 <expand macro="additionally_SNP_process" />
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
82 </section>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
83 </section>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
84 </inputs>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
85 <outputs>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
86 <data name="out_scatter_file" format="png" label="${tool.name} on ${on_string}: diagram pdf file" from_work_dir="sample-scatter.png" />
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
87 </outputs>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
88 <tests>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
89 <test expect_num_outputs="1">
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
90 <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" />
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
91 <param name="zygosity_freq" value="0.25" />
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
92 <param name="by_bin" value="1" />
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
93 <output name="out_scatter_file" file="sample-scatter.png" ftype="png" compare="sim_size">
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
94 <assert_contents><has_size value="12000" delta="5000" /></assert_contents>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
95 </output>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
96 </test>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
97 </tests>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
98 <help><![CDATA[
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
99 Plot bin-level log2 coverages and segmentation calls together. Without any further arguments,
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
100 this plots the genome-wide copy number in a form familiar to those who have used array CGH.
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
101 ]]></help>
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
102 <expand macro="citations" />
ec9731970f8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
103 </tool>