Mercurial > repos > iuc > colibread_kissplice
changeset 6:7c02beb8ba3d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
| author | iuc |
|---|---|
| date | Sat, 05 Oct 2024 19:54:14 +0000 |
| parents | 7d4435f9c77d |
| children | |
| files | kissplice.xml macros.xml |
| diffstat | 2 files changed, 43 insertions(+), 23 deletions(-) [+] |
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--- a/kissplice.xml Thu May 06 12:44:17 2021 +0000 +++ b/kissplice.xml Sat Oct 05 19:54:14 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="kissplice" name="KisSplice" version="2.4.0+galaxy0" profile="@PROFILE@"> +<tool id="kissplice" name="KisSplice" version="2.4.0+galaxy1" profile="@PROFILE@"> <description>is a local transcriptome assembler for SNPs, indels and AS events</description> <macros> <import>macros.xml</import> @@ -26,7 +26,7 @@ <param argument="-k" type="integer" value="41" label="K-mer length" /> <param argument="-c" type="integer" value="2" label="K-mers present strictly less than this number of times in the dataset will be discarded (integer value required)" /> <param argument="-C" type="float" value="0.05" label="Edges with relative coverage below this number are removed (value in [0,1) required)" /> - <param name="output_context" argument="--output-context" type="boolean" checked="false" truevalue="--output-context" falsevalue="" label="Output the maximum non-ambiguous context of each event" /> + <param argument="--output-context" type="boolean" checked="false" truevalue="--output-context" falsevalue="" label="Output the maximum non-ambiguous context of each event" /> <param argument="--counts" type="select" label="Selecting how the counts will be reported"> <option value="0">Total counts</option> <option value="1">Counts on junctions</option> @@ -38,30 +38,61 @@ </param> </inputs> <outputs> - <data name="type0a" format="fasta" label="Single SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0a.fa"> + <data name="type0a" format="fasta" label="${tool.name} on ${on_string}: Single SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0a.fa"> <filter>output_option == 'all_files'</filter> </data> - <data name="type0b" format="fasta" label="Multiple SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0b.fa"> + <data name="type0b" format="fasta" label="${tool.name} on ${on_string}: Multiple SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0b.fa"> <filter>output_option == 'all_files'</filter> </data> - <data name="type1" format="fasta" label="Alternative splicing events" from_work_dir="results/*_coherents_type_1.fa"/> - <data name="type2" format="fasta" label="Inexact tandem repeats" from_work_dir="results/*_coherents_type_2.fa"> + <data name="type1" format="fasta" label="${tool.name} on ${on_string}: Alternative splicing events" from_work_dir="results/*_coherents_type_1.fa"/> + <data name="type2" format="fasta" label="${tool.name} on ${on_string}: Inexact tandem repeats" from_work_dir="results/*_coherents_type_2.fa"> <filter>output_option == 'all_files'</filter> </data> - <data name="type3" format="fasta" label="Short indels" from_work_dir="results/*_coherents_type_3.fa"> + <data name="type3" format="fasta" label="${tool.name} on ${on_string}: Short indels" from_work_dir="results/*_coherents_type_3.fa"> <filter>output_option == 'all_files'</filter> </data> - <data name="type4" format="fasta" label="Other events" from_work_dir="results/*_coherents_type_4.fa"> + <data name="type4" format="fasta" label="${tool.name} on ${on_string}: Other events" from_work_dir="results/*_coherents_type_4.fa"> <filter>output_option == 'all_files'</filter> </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" /> <param name="k" value="25"/> <param name="output_option" value="alternative_file" /> <output name="type1" file="kissplice/alternative_splicing.fa"/> </test> + <test expect_num_outputs="6"> + <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" /> + <param name="k" value="25"/> + <param name="output_option" value="all_files" /> + <output name="type0a"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + <output name="type0b"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + <output name="type1" file="kissplice/alternative_splicing.fa"/> + <output name="type2"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + <output name="type3"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + <output name="type4"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ @@ -82,17 +113,7 @@ ]]></help> <expand macro="citations"> - <citation type="bibtex"> - @article{PMID:22537044, - author = {Sacomoto, G. A. and Kielbassa, J. and Chikhi, R. and Uricaru, R. and Antoniou, P. and Sagot, M. F. and Peterlongo, P. and Lacroix, V.}, - title = {KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.}, - journal = {BMC Bioinformatics}, - year = {2012}, - volume = {13 Suppl 6}, - pages = {S5}, - url = {http://www.ncbi.nlm.nih.gov/pubmed/22537044}, - } - </citation> + <citation type="doi">10.1186/1471-2105-13-S6-S5</citation> </expand> </tool>
--- a/macros.xml Thu May 06 12:44:17 2021 +0000 +++ b/macros.xml Sat Oct 05 19:54:14 2024 +0000 @@ -1,11 +1,10 @@ <macros> - <token name="@DISCOSNP_VERSION@">2.5.4</token> - <token name="@PROFILE@">20.01</token> + <token name="@PROFILE@">23.1</token> <xml name="discosnp_requirements"> <requirements> - <requirement type="package" version="@DISCOSNP_VERSION@">discosnp</requirement> + <requirement type="package" version="@TOOL_VERSION@">discosnp</requirement> </requirements> </xml>