Mercurial > repos > iuc > cnvkit_export_cdt

annotate cdt.xml @ 0:5406089c2db7 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 51995527835d18a4a3a498b140382ce433f19a71
author iuc
date Mon, 20 Jan 2025 16:40:16 +0000
parents
children 21a1d65e26ba
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
1 <tool id="cnvkit_export_cdt" name="CNVkit Export CDT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
2 <description>Convert log2 ratios to Clustered Data Table (CDT)</description>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
3 <macros>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
4 <import>macros.xml</import>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
5 </macros>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
6 <expand macro="xrefs"/>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
7 <expand macro="creators"/>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
8 <expand macro="requirements"/>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
10 ln -s '$input_segmented_file' ./sample.cnr &&
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
11 cnvkit.py export cdt
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
12 ./sample.cnr
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
13 --output sample.cnv.cdt
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
14 ]]></command>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
15 <inputs>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
16 <param name="input_segmented_file" type="data" format="tabular" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
17 </inputs>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
18 <outputs>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
19 <data name="CNVs_cdt" format="cdt" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.cdt" />
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
20 </outputs>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
21 <tests>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
22 <test expect_num_outputs="1">
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
23 <param name="input_segmented_file" ftype="tabular" value="sample.cnr" />
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
24 <output name="CNVs_cdt" file="sample.cnv.cdt" />
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
25 </test>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
26 </tests>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
27 <help><![CDATA[
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
28 This tool converts CNVkit log2 copy ratio data to the CDT format, which is compatible with Java TreeView for visualisation and hierarchical clustering.
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
29 The conversion enables efficient exploration and interpretation of genomic copy number variations.
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
30 ]]></help>
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
31 <expand macro="citations" />
5406089c2db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
parents:
diff changeset
32 </tool>