| Previous changeset 21:7bef1cd4d2ad (2022-10-10) |
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Commit message:
planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 7c372dde3a9a59818eeabce66742c9f448ba0307 |
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modified:
CLIFinder.xml README.rst script/js/jquery.min.js |
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| diff -r 7bef1cd4d2ad -r e50f9ebde308 CLIFinder.xml --- a/CLIFinder.xml Mon Oct 10 12:14:45 2022 +0000 +++ b/CLIFinder.xml Wed Apr 10 10:24:17 2024 +0000 |
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| @@ -201,19 +201,19 @@ <when value="false" /> </conditional> </section> - <param argument="--rmsk" name="rmsk" type="data" format="tabular" label="Tab-delimited text file (with headers) containing reference repeat sequences (e.g. rmsk track from UCSC)"/> - <param argument="--refseq" name="refseq" type="data" format="tabular" label="Tab-delimited file (with headers) containing reference genes (e.g. RefGene.txt from UCSC)"/> + <param argument="--rmsk" type="data" format="tabular" label="Tab-delimited text file (with headers) containing reference repeat sequences (e.g. rmsk track from UCSC)"/> + <param argument="--refseq" type="data" format="tabular" label="Tab-delimited file (with headers) containing reference genes (e.g. RefGene.txt from UCSC)"/> <param name="BDir" type="select" > <option value="0">Undirectional libraries</option> <option value="1">TEs sequences in first read in pair</option> <option value="2">TEs sequences in second read in pair</option> </param> <param argument="--size_read" name="size" type="integer" value="100" label="Reads size"/> - <param argument="--size_insert" name="size_insert" type="integer" value="250" label="Maximum insert size (bp)"/> - <param argument="--min_L1" name="min_L1" type="integer" value="50" label="Minimun bp mapping on selected TEs database"/> - <param argument="--mis_L1" name="mis_L1" type="integer" value="1" label="Number of mismatches tolerated in TEs mapping sequences"/> - <param argument="--min_unique" name="min_unique" type="integer" value="33" label="Minimum consecutive bp corresponding to a unique sequence"/> - <param argument="--species" name="species" type="text" value="human" label="Species or clade of the input sequence (the species name must be a valid NCBI Taxonomy Database species name and be contained in the RepeatMasker repeat database)"/> + <param argument="--size_insert" type="integer" value="250" label="Maximum insert size (bp)"/> + <param argument="--min_L1" type="integer" value="50" label="Minimun bp mapping on selected TEs database"/> + <param argument="--mis_L1" type="integer" value="1" label="Number of mismatches tolerated in TEs mapping sequences"/> + <param argument="--min_unique" type="integer" value="33" label="Minimum consecutive bp corresponding to a unique sequence"/> + <param argument="--species" type="text" value="human" label="Species or clade of the input sequence (the species name must be a valid NCBI Taxonomy Database species name and be contained in the RepeatMasker repeat database)"/> </inputs> <outputs> <data format="html" name="chimerae" label="${tool.name}_on_${on_string}"/> |
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| diff -r 7bef1cd4d2ad -r e50f9ebde308 README.rst --- a/README.rst Mon Oct 10 12:14:45 2022 +0000 +++ b/README.rst Wed Apr 10 10:24:17 2024 +0000 |
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| @@ -1,7 +1,7 @@ -.. image:: https://travis-ci.org/GReD-Clermont/CLIFinder.svg?branch=master - :target: https://travis-ci.org/GReD-Clermont/CLIFinder +.. image:: https://github.com/GReD-Clermont/CLIFinder/actions/workflows/planemo.yml/badge.svg + :target: https://github.com/GReD-Clermont/CLIFinder/actions/workflows/planemo.yml -CLIFinder v0.5.1 +CLIFinder v0.5.2 ================ @@ -9,8 +9,8 @@ ----------- L1 Chimeric Transcripts (LCTs) are transcribed from LINE 1 antisense promoter and include the L1 5’UTR sequence in antisense orientation followed by the adjacent genomic region. -CLIFinder v0.5.1 is a Galaxy tool, specifically designed to identify potential LCTs from one or several oriented RNA-seq paired-end reads in the human genome. -CLIFinder v0.5.1 is customizable to detect transcripts initiated by different types of repeat elements. +CLIFinder v0.5.2 is a Galaxy tool, specifically designed to identify potential LCTs from one or several oriented RNA-seq paired-end reads in the human genome. +CLIFinder v0.5.2 is customizable to detect transcripts initiated by different types of repeat elements. |
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| diff -r 7bef1cd4d2ad -r e50f9ebde308 script/js/jquery.min.js --- a/script/js/jquery.min.js Mon Oct 10 12:14:45 2022 +0000 +++ b/script/js/jquery.min.js Wed Apr 10 10:24:17 2024 +0000 |
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