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comparison allele-counts.xml @ 9:6cc488e11544 draft

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"planemo upload for repository https://github.com/galaxyproject/dunovo commit 5a2e08bc1213b0437d0adcb45f7f431bd3c735f4"
author nick
date Tue, 31 Mar 2020 05:09:12 -0400
parents a72277535a2c
children 7f19e8c03358
comparison
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8:411adeff1eec 9:6cc488e11544
1 <tool id="allele_counts_1" version="1.2" name="Variant Annotator"> 1 <tool id="allele_counts_1" version="1.3" name="Variant Annotator">
2 <description> process variant counts</description> 2 <description> process variant counts</description>
3 <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt 3 <stdio>
4 <exit_code range="1:" level="fatal" />
5 <exit_code range=":-1" level="fatal" />
6 </stdio>
7 <command>allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt
4 #if $seed: 8 #if $seed:
5 -r $seed 9 -r $seed
6 #end if 10 #end if
7 </command> 11 </command>
8 <inputs> 12 <inputs>
13 <param name="stranded" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output stranded base counts" /> 17 <param name="stranded" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output stranded base counts" />
14 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="True" label="Write header line" /> 18 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="True" label="Write header line" />
15 <param name="seed" type="text" value="" label="PRNG seed" /> 19 <param name="seed" type="text" value="" label="PRNG seed" />
16 </inputs> 20 </inputs>
17 <outputs> 21 <outputs>
18 <data name="output" format="tabular"/> 22 <data name="output" format="tabular" />
19 </outputs> 23 </outputs>
20 <stdio>
21 <exit_code range="1:" err_level="fatal"/>
22 <exit_code range=":-1" err_level="fatal"/>
23 </stdio>
24 24
25 <tests> 25 <tests>
26 <test> 26 <test>
27 <param name="input" value="tests/artificial.vcf.in" /> 27 <param name="input" value="tests/artificial.vcf.in" />
28 <param name="freq" value="10" /> 28 <param name="freq" value="10" />
112 112
113 Additionally, a measure of strand bias is given in the last column. This is calculated using the method of Guo et al., 2012. A value of "." is given when there is no valid result of the calculation due to a zero denominator. This occurs when there are no reads on one of the strands, or when there is no minor allele. 113 Additionally, a measure of strand bias is given in the last column. This is calculated using the method of Guo et al., 2012. A value of "." is given when there is no valid result of the calculation due to a zero denominator. This occurs when there are no reads on one of the strands, or when there is no minor allele.
114 114
115 </help> 115 </help>
116 116
117 <citations>
118 <citation type="bibtex">
119 @article{Blankenberg2014,
120 author = {Blankenberg, Daniel and {Von Kuster}, Gregory and Bouvier, Emil and Baker, Dannon and Afgan, Enis and Stoler, Nicholas and Taylor, James and Nekrutenko, Anton},
121 doi = {10.1186/gb4161},
122 issn = {1465-6906},
123 journal = {Genome Biology},
124 keywords = {galaxy},
125 number = {2},
126 pages = {403},
127 title = {{Dissemination of scientific software with Galaxy ToolShed}},
128 url = {http://genomebiology.biomedcentral.com/articles/10.1186/gb4161},
129 volume = {15},
130 year = {2014}
131 }
132 </citation>
133 <citation type="bibtex">
134 @article{Dickins2014,
135 archivePrefix = {arXiv},
136 arxivId = {15334406},
137 author = {Dickins, Benjamin and Rebolledo-Jaramillo, Boris and Su, Marcia Shu Wei and Paul, Ian M and Blankenberg, Daniel and Stoler, Nicholas and Makova, Kateryna D and Nekrutenko, Anton},
138 doi = {10.2144/000114146},
139 eprint = {15334406},
140 isbn = {5049880467},
141 issn = {19409818},
142 journal = {BioTechniques},
143 number = {3},
144 pages = {134--141},
145 pmid = {24641477},
146 title = {{Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach}},
147 volume = {56},
148 year = {2014}
149 }
150 </citation>
151 </citations>
152
117 </tool> 153 </tool>