Mercurial > repos > nick > allele_counts
diff allele-counts.xml @ 9:6cc488e11544 draft
"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 |
line wrap: on
line diff
--- a/allele-counts.xml Tue Aug 23 02:30:56 2016 -0400 +++ b/allele-counts.xml Tue Mar 31 05:09:12 2020 -0400 @@ -1,6 +1,10 @@ -<tool id="allele_counts_1" version="1.2" name="Variant Annotator"> +<tool id="allele_counts_1" version="1.3" name="Variant Annotator"> <description> process variant counts</description> - <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt + <stdio> + <exit_code range="1:" level="fatal" /> + <exit_code range=":-1" level="fatal" /> + </stdio> + <command>allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt #if $seed: -r $seed #end if @@ -15,12 +19,8 @@ <param name="seed" type="text" value="" label="PRNG seed" /> </inputs> <outputs> - <data name="output" format="tabular"/> + <data name="output" format="tabular" /> </outputs> - <stdio> - <exit_code range="1:" err_level="fatal"/> - <exit_code range=":-1" err_level="fatal"/> - </stdio> <tests> <test> @@ -114,4 +114,40 @@ </help> + <citations> + <citation type="bibtex"> + @article{Blankenberg2014, + 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}, + doi = {10.1186/gb4161}, + issn = {1465-6906}, + journal = {Genome Biology}, + keywords = {galaxy}, + number = {2}, + pages = {403}, + title = {{Dissemination of scientific software with Galaxy ToolShed}}, + url = {http://genomebiology.biomedcentral.com/articles/10.1186/gb4161}, + volume = {15}, + year = {2014} + } + </citation> + <citation type="bibtex"> + @article{Dickins2014, + archivePrefix = {arXiv}, + arxivId = {15334406}, + 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}, + doi = {10.2144/000114146}, + eprint = {15334406}, + isbn = {5049880467}, + issn = {19409818}, + journal = {BioTechniques}, + number = {3}, + pages = {134--141}, + pmid = {24641477}, + title = {{Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach}}, + volume = {56}, + year = {2014} + } + </citation> + </citations> + </tool>