Mercurial > repos > iuc > cnvkit_breaks
comparison breaks.xml @ 0:27b8228a4d84 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
| author | iuc |
|---|---|
| date | Fri, 29 Sep 2023 15:37:33 +0000 |
| parents | |
| children | 382f61e50156 |
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| -1:000000000000 | 0:27b8228a4d84 |
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| 1 <tool id="cnvkit_breaks" name="CNVkit Breaks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |
| 2 <description>List the targeted genes with segmentaion breakpoint</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="xrefs"/> | |
| 7 <expand macro="creators_and_zahra"/> | |
| 8 <expand macro="requirements"/> | |
| 9 <command detect_errors="exit_code"><![CDATA[ | |
| 10 ln -s '$input_filename_file' ./sample.cnr && | |
| 11 ln -s '$input_segment_file' ./sample.cns && | |
| 12 cnvkit.py breaks | |
| 13 ./sample.cnr | |
| 14 ./sample.cns | |
| 15 --output gene-breaks.txt | |
| 16 #if $min_probes | |
| 17 --min-probes $min_probes | |
| 18 #end if | |
| 19 ]]></command> | |
| 20 <inputs> | |
| 21 <param name="input_filename_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="The output of the CNVkit fix" /> | |
| 22 <param name="input_segment_file" type="data" format="tabular" label="CN segmentation calls cnn file" help="The output of the CNVkit segment" /> | |
| 23 <param argument="--min-probes" optional="true" type="integer" label="Minimum propes" value="1" help="Minimum number of covered probes to label a gene" /> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data name="gene_breaks" format="text" label="${tool.name} on ${on_string}:genes with copy number breakpoints" from_work_dir="gene-breaks.txt" /> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test expect_num_outputs="1"> | |
| 30 <param name="input_filename_file" ftype="tabular" value="sample.cnr" /> | |
| 31 <param name="input_segment_file" ftype="tabular" value="sample.cns" /> | |
| 32 <param name="min_probes" value="1" /> | |
| 33 <output name="gene_breaks"> | |
| 34 <assert_contents><has_text text="chromosome"/></assert_contents> | |
| 35 </output> | |
| 36 </test> | |
| 37 </tests> | |
| 38 <help><![CDATA[ | |
| 39 | |
| 40 Identify genes in which: | |
| 41 (I) an unbalanced fusion or other structural rearrangement breakpoint occured | |
| 42 (II) CNV calling is simply difficult due to an inconsistent copy number signal | |
| 43 | |
| 44 The breaks output is a text table of tab-separated values, which is amenable to further processing by | |
| 45 scripts and standard Unix tools such as grep, sort, cut and awk. | |
| 46 ]]></help> | |
| 47 <expand macro="citations" /> | |
| 48 </tool> | |
| 49 | |
| 50 | |
| 51 | |
| 52 |