Mercurial > repos > bgruening > cpat
changeset 0:8e9e228c54c4 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cpat commit 1903b0d45ff57d20d6e3a9b95fa55ad6d4a0f345
| author | bgruening |
|---|---|
| date | Wed, 01 Feb 2023 19:22:06 +0000 |
| parents | |
| children | 1ac12c0cc7a0 |
| files | cpat.xml test-data/sequences.fasta.gz test-data/test01_no_orgs.txt test-data/test02_no_orgs.txt |
| diffstat | 4 files changed, 173 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpat.xml Wed Feb 01 19:22:06 2023 +0000 @@ -0,0 +1,169 @@ +<tool id="cpat" name="CPAT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>coding potential assessment</description> + <macros> + <token name="@TOOL_VERSION@">3.0.4</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">cpat</requirement> + </requirements> + <version_command>cpat --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + #set $gen_ext = $gene.ext + ln -s '${gene}' './gene_sequences.${gen_ext}' && + #set $cod_ext = $c.ext + ln -s '${c}' './conding_sequences.${cod_ext}' && + #set $ncod_ext = $n.ext + ln -s '${n}' './nonconding_sequences.${ncod_ext}' && + #set $ref_ext = $r.ext + ln -s '${r}' './referece.${ref_ext}' && + make_hexamer_tab.py + -c './conding_sequences.${cod_ext}' + -n './nonconding_sequences.${ncod_ext}' > './hexamer.tsv' && + make_logitModel.py + -x './hexamer.tsv' + -c './conding_sequences.${cod_ext}' + -n './nonconding_sequences.${ncod_ext}' + -r './referece.${ref_ext}' + --start='${start}' + --stop='${stop}' + --min-orf=$min_orf_model + -o './logit_model' && + cpat.py --verbose + -x './hexamer.tsv' + -d './logit_model.logit.RData' + -g './gene_sequences.${gen_ext}' + --top-orf=$top_orf + --antisense + --start='${start}' + --stop='${stop}' + --min-orf=$min_orf_cpat + $antisense + --top-orf=$top_orf + --best-orf=$best_orf + -o 'output' + ]]> + </command> + <inputs> + <param argument="--gene" type="data" format="fasta,fasta.gz" label="Query nucletide sequences" help="It is recommended to use short and unique sequence identifiers"/> + <param argument="-r" type="data" format="fasta,fasta.gz" label="Reference genome" help="Reference genome sequences in FASTA format" /> + <param argument="-c" type="data" format="fasta,fasta.gz" label="Coding sequences file" help="Coding sequence (must be CDS without UTR, i.e. from start coden to stop coden) in FASTA format" /> + <param argument="-n" type="data" format="fasta,fasta.gz" label="Non coding sequeces file" help="Noncoding sequences in FASTA format" /> + <param argument="--start" type="text" value="ATG" label="Start codon"> + <sanitizer invalid_char=""> + <valid initial="string.letters"/> + </sanitizer> + <validator type="regex">[a-zA-Z]+</validator> + </param> + <param argument="--stop" type="text" value="TAG,TAA,TGA" label="Stop codons"> + <sanitizer invalid_char=""> + <valid initial="string.letters"> + <add value="," /> + </valid> + </sanitizer> + <validator type="regex">[a-zA-Z,]+</validator> + </param> + <param argument="--min-orf" name="min_orf_model" type="integer" min="0" value="30" label="Minimum ORF length" help="Minimum ORF length in nucleotides" /> + <param argument="--min-orf" name="min_orf_cpat" type="integer" min="0" value="75" label="Minimum ORF length" help="Minimum ORF length in nucleotides" /> + <param argument="--antisense" type="boolean" truevalue="--antisense" falsevalue="" checked="false" label="Search for ORFs from the anti-sense strand"/> + <param argument="--top-orf" type="integer" min="0" value="5" label="Number of ORF candidates reported" help="RNAs may have dozens of putative ORFs, in most cases, the real ORF + is ranked (by size) in the top several" /> + <param argument="--best-orf" type="select" label="Criteria to select the best ORF"> + <option value="l">ORF length (l)</option> + <option value="p" selected="true">Coding probability (p)</option> + </param> + </inputs> + <outputs> + <data name="orf_seqs" format="fasta" from_work_dir="output.ORF_seqs.fa" label="${tool.name} on ${on_string}: ORF sequences (FASTA)"/> + <data name="orf_seqs_prob" format="tsv" from_work_dir="output.ORF_prob.tsv" label="${tool.name} on ${on_string}: ORF probabiities (TSV)"/> + <data name="orf_seqs_prob_best" format="tsv" from_work_dir="output.ORF_prob.best.tsv" label="${tool.name} on ${on_string}: ORF best probabilities (TSV)"/> + <data name="no_orf_seqs" format="txt" from_work_dir="output.no_ORF.txt" label="${tool.name} on ${on_string}: no ORFs (TXT)"/> + </outputs> + <tests> + <test expect_num_outputs="4"> + <param name="gene" value="sequences.fasta.gz"/> + <param name="r" value="sequences.fasta.gz"/> + <param name="c" value="sequences.fasta.gz"/> + <param name="n" value="sequences.fasta.gz"/> + <param name="start" value="ATG"/> + <param name="stop" value="TAG,TAA,TGA"/> + <param name="min_orf_model" value="30"/> + <param name="min_orf_cpat" value="75"/> + <param name="antisense" value="false"/> + <param name="top_orf" value="5"/> + <param name="best_orf" value="l"/> + <output name="orf_seqs" ftype="fasta"> + <assert_contents> + <has_text text=">ENST00000616016.5_ORF_1"/> + <has_n_lines n="41009"/> + </assert_contents> + </output> + <output name="orf_seqs_prob" ftype="tsv"> + <assert_contents> + <has_text text="ENST00000616016.5_ORF_1"/> + <has_n_lines n="6237"/> + </assert_contents> + </output> + <output name="orf_seqs_prob_best" ftype="tsv"> + <assert_contents> + <has_text text="ENST00000683977.1"/> + <has_n_lines n="1301" delta="5"/> + </assert_contents> + </output> + <output name="no_orf_seqs" file="test01_no_orgs.txt" ftype="txt"/> + </test> + <test expect_num_outputs="4"> + <param name="gene" value="sequences.fasta.gz"/> + <param name="r" value="sequences.fasta.gz"/> + <param name="c" value="sequences.fasta.gz"/> + <param name="n" value="sequences.fasta.gz"/> + <param name="start" value="ATG"/> + <param name="stop" value="TAG,TAA,TGA"/> + <param name="min_orf_model" value="15"/> + <param name="min_orf_cpat" value="60"/> + <param name="antisense" value="true"/> + <param name="top_orf" value="10"/> + <param name="best_orf" value="p"/> + <output name="orf_seqs" ftype="fasta"> + <assert_contents> + <has_text text=">ENST00000616016.5_ORF_1"/> + <has_n_lines n="57357"/> + </assert_contents> + </output> + <output name="orf_seqs_prob" ftype="tsv"> + <assert_contents> + <has_text text="ENST00000616016.5_ORF_1"/> + <has_n_lines n="11667"/> + </assert_contents> + </output> + <output name="orf_seqs_prob_best" ftype="tsv"> + <assert_contents> + <has_text text="ENST00000683977.1"/> + <has_n_lines n="1301"/> + </assert_contents> + </output> + <output name="no_orf_seqs" file="test02_no_orgs.txt" ftype="txt"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**Purpose** + +CPAT is a bioinformatics tool to predict RNAs coding probability based on the RNA sequence characteristics. To achieve this goal, CPAT calculates scores of these 4 linguistic features +from a set of known protein-coding genes and another set of non-coding genes. + +- ORF size +- ORF coverage +- Fickett TESTCODE +- Hexamer usage bias + +CPAT will then builds a logistic regression model using these 4 features as predictor variables and the “protein-coding status” as the response variable. After evaluating the performance +and determining the probability cutoff, the model can be used to predict new RNA sequences. + +]]></help> + <citations> + <citation type="doi">10.1093/nar/gkt006</citation> + </citations> +</tool>