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comparison exomedepth.xml @ 7:45af4a9748cf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth commit 91a0182476a7fc26be7bef1677790518c4e88348"
author iuc
date Fri, 08 Nov 2019 13:25:44 -0500
parents 165732ee5a48
children 5d60331757d3
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6:165732ee5a48 7:45af4a9748cf
1 <tool id="exomedepth" name="ExomeDepth" version="1.0.0"> 1 <tool id="exomedepth" name="ExomeDepth" version="1.1.0">
2 <description>cnv caller</description> 2 <description>Calls copy number variants (CNVs) from targeted sequence data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.10">r-exomedepth</requirement> 4 <requirement type="package" version="1.1.10">r-exomedepth</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <version_command><![CDATA[
7 R CMD BATCH --no-save --no-restore '--args mypars="$args_file"' $__tool_directory__/exomedepth.R 7 echo $(R --version | grep version | grep -v GNU)", ExomeDepth version" $(R --vanilla --slave -e "library(ExomeDepth); cat(sessionInfo()\$otherPkgs\$ExomeDepth\$Version)")
8 </command> 8 ]]></version_command>
9 <inputs> 9 <command detect_errors="exit_code"><![CDATA[
10 <param format="bed" name="targetFile" type="data" label="Target regions (BED)"> 10 Rscript '${__tool_directory__}/exomedepth.R' '$args_file'
11 <validator type="unspecified_build" /> 11 ]]></command>
12 </param> 12 <configfiles>
13 <param name="test_vs_ref" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Call CNVs using 1st sample as test" help="If checked, the tool will call CNVs in the first sample vs all the others. If unchecked, an all vs all CNV call will be performed" /> 13 <configfile name="args_file"><![CDATA[
14 <repeat name="inputs" title="BAM" min="2" help="Need to add more files? Use controls below."> 14 target=$targetFile
15 <param format="bam" name="input" type="data" label="BAM file">
16 <options>
17 <filter type="data_meta" ref="targetFile" key="dbkey"/>
18 </options>
19 </param>
20 <param name="label" type="text" size="30" value="" label="Label" help="Label to use in the output. If not given, the dataset name will be used instead">
21 <validator type="regex" message="Spaces are not allowed">^\S*$</validator>
22 </param>
23 </repeat>
24 <param name="transition_probability" size="10" type="float" value="0.0001" label="Transition probability" help="Transition probability of the hidden Markov Chain from the normal copy number state to either a deletion or a duplication. The default value (0.0001) expects approximately 20 CNVs genome-wide" />
25 </inputs>
26
27 <configfiles>
28 <configfile name="args_file">target=$targetFile
29 test_vs_ref=$test_vs_ref 15 test_vs_ref=$test_vs_ref
30 #for $i in $inputs 16 #for $i in $inputs
31 bam=${i.input} 17 bam=${i.input}
32 bam_bai=${i.input.metadata.bam_index} 18 bam_bai=${i.input.metadata.bam_index}
33 #if str($i.label.value) != "": 19 #if str($i.label.value) != "":
36 bam_label=${i.input.dataset.name} 22 bam_label=${i.input.dataset.name}
37 #end if 23 #end if
38 #end for 24 #end for
39 trans_prob=$transition_probability 25 trans_prob=$transition_probability
40 output=$output 26 output=$output
41 </configfile> 27 ]]></configfile>
42 </configfiles> 28 </configfiles>
43 <outputs> 29 <inputs>
44 <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> 30 <param name="targetFile" type="data" format="bed" label="Target regions (BED)">
45 </outputs> 31 <validator type="unspecified_build" />
46 <help> 32 </param>
47 33 <param name="test_vs_ref" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Call CNVs using 1st sample as test" help="If checked, the tool will call CNVs in the first sample vs all the others. If unchecked, an all vs all CNV call will be performed" />
34 <repeat name="inputs" title="BAM" min="2" help="Need to add more files? Use controls below.">
35 <param name="input" type="data" format="bam" label="BAM file">
36 <options>
37 <filter type="data_meta" ref="targetFile" key="dbkey"/>
38 </options>
39 </param>
40 <param name="label" type="text" size="30" value="" label="Label" help="Label to use in the output. If not given, the dataset name will be used instead">
41 <validator type="regex" message="Spaces are not allowed">^\S*$</validator>
42 </param>
43 </repeat>
44 <param name="transition_probability" size="10" type="float" value="0.0001" label="Transition probability" help="Transition probability of the hidden Markov Chain from the normal copy number state to either a deletion or a duplication. The default value (0.0001) expects approximately 20 CNVs genome-wide" />
45 </inputs>
46 <outputs>
47 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
48 </outputs>
49 <tests>
50 <test>
51 <param name="targetFile" value="CNV_TruSeq_Chr2.bed" dbkey="hg19" ftype="bed"/>
52 <param name="test_vs_ref" value="True"/>
53 <repeat name="inputs">
54 <param name="input" value="CNV_case_small.bam"/>
55 </repeat>
56 <repeat name="inputs">
57 <param name="input" value="CNV_control_small.bam"/>
58 </repeat>
59 <param name="transition_probability" value="0.5"/>
60 <output name="output">
61 <assert_contents>
62 <has_text text="chr2" />
63 <has_text text="97890544" />
64 <has_text text="97890616" />
65 <has_text text="deletion" />
66 <has_text text="CNV_case_small" />
67 </assert_contents>
68 </output>
69 </test>
70 </tests>
71 <help><![CDATA[
48 .. class:: warningmark 72 .. class:: warningmark
49 73
50 **Warning about counts for chromosome X** 74 **Warning about counts for chromosome X**
51 75
52 Calling CNVs on the X chromosome can create issues if the exome sample of interest and the reference exome 76 Calling CNVs on the X chromosome can create issues if the exome sample of interest and the reference exome
90 The ideas used in this package are of course not specific to exome sequencing and could be applied to other 114 The ideas used in this package are of course not specific to exome sequencing and could be applied to other
91 targeted sequencing datasets, as long as they contain a sufficiently large number of exons to estimate the parameters 115 targeted sequencing datasets, as long as they contain a sufficiently large number of exons to estimate the parameters
92 (at least 20 genes, say, but probably more would be useful). Also note that PCR based enrichment studies are often 116 (at least 20 genes, say, but probably more would be useful). Also note that PCR based enrichment studies are often
93 not well suited for this type of read depth analysis. The reason is that as the number of cycles is often set to a high 117 not well suited for this type of read depth analysis. The reason is that as the number of cycles is often set to a high
94 number in order to equalize the representation of each amplicon, which can discard the CNV information. 118 number in order to equalize the representation of each amplicon, which can discard the CNV information.
95 119 ]]></help>
96 **License and citation**
97
98 This Galaxy tool is Copyright © 2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
99
100 .. _CRS4 Srl.: http://www.crs4.it/
101 .. _MIT license: http://opensource.org/licenses/MIT
102
103 You can use this tool only if you agree to the license terms of: `ExomeDepth`_.
104
105 .. _ExomeDepth: http://cran.r-project.org/web/packages/ExomeDepth/
106
107 If you use this tool, please cite:
108
109 - |Cuccuru2014|_
110 - |Plagnol2012|_.
111
112 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
113 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
114 .. |Plagnol2012| replace:: Plagnol, V., *et al.* (2012) A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. *Bioinformatics* 28(21), 2747-2754
115 .. _Plagnol2012: http://bioinformatics.oxfordjournals.org/content/28/21/2747
116 </help>
117 <citations> 120 <citations>
118 <citation type="doi">10.1093/bioinformatics/btu135</citation> 121 <citation type="doi">10.1093/bioinformatics/btu135</citation>
119 <citation type="doi">10.1093/bioinformatics/bts526</citation> 122 <citation type="doi">10.1093/bioinformatics/bts526</citation>
120 </citations> 123 </citations>
121 </tool> 124 </tool>