Mercurial > repos > leomrtns > dfast
diff dfast.xml @ 0:6ddc8a6503e7 draft default tip
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/dfast
author | leomrtns |
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date | Thu, 03 Oct 2019 12:41:36 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dfast.xml Thu Oct 03 12:41:36 2019 -0400 @@ -0,0 +1,111 @@ +<tool id="dfast" name="dfast" version="@VERSION@"> + <description>prokaryotic genome annotation</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + #import re + #if $ortho.use + #set $ref_set_str = '' + #set $divisor = '' + #for $i_file in $ortho.refs: + #set $ref_set_str = $ref_set_str + $divisor + "{}".format($i_file) + #set $divisor = ';' ### will create "A ; B ; C " + #end for + #end if + #if $genome_input.is_of_type('fasta'): + ln -s ${genome_input} in.fasta && + #elif $genome_input.is_of_type('fasta.gz'): + gunzip -c ${genome_input} > in.fasta && + #elif $genome_input.is_of_type('fasta.bz2'): + bunzip2 -c ${genome_input} > in.fasta && + #end if + dfast -g in.fasta + -o OUT + --cpu \${GALAXY_SLOTS:-1} + --aligner ${aligner} + --gcode ${gcode} + --use_original_name ${use_orig_name} + --sort_sequence ${sort_sequence} + --use_separate_tags ${separate_tags} + #if str($min_length) != "" + --minimum_length ${min_length} + #end if + #if $ortho.use + --references "${ref_set_str}" + #end if + ${fix_origin} + ]]></command> + <inputs> + <param name="genome_input" multiple="false" format="fasta, fasta.gz, fasta.bz2" type="data" label="Genome to be annotated, in fasta format (can be zipped)"/> + + <param name="aligner" type="select" label="Aligner" help="Safer to leave the default (ghostx)"> + <option value="ghostx" selected="true">ghostx (default)</option> + <option value="blastp">blastp (experimental, since didn't pass local tests) </option> + </param> + + <param name="gcode" type="select" label="Genetic code"> + <option value="11" selected="true">Default</option> + <option value="4">Mycoplasma</option> + </param> + + <param name="use_orig_name" type="boolean" truevalue="t" falsevalue="f" checked="false" help="--use_original_name" label="Use original sequence names in a query FASTA file"/> + + <param name="sort_sequence" type="boolean" truevalue="t" falsevalue="f" checked="true" help="--sort_sequence" label="Sort sequences by length"/> + + <param name="min_length" type="integer" label="Minimum sequence length (default:200)" help="--minimum_length" optional="true" /> + + <param name="separate_tags" type="boolean" truevalue="t" falsevalue="f" checked="true" help="--use_separate_tags" label="Use separate tags according to feature types"/> + + <param name="fix_origin" type="boolean" truevalue="--fix_origin" falsevalue="" checked="false" help="--fix_origin" + label="Rotate/flip the chromosome so that the dnaA gene comes first. (ONLY FOR A FINISHED GENOME)" /> + + <conditional name="ortho"> + <param name="use" type="boolean" checked="false" help="--references" label="orthologous gene assignment with OrthoSearch"/> + <when value="true"> + <param name="refs" type="data" multiple="true" format="genbank,embl,asn1" label="One or more genbank reference genomes"> + <help><![CDATA[ + OrthoSearch conducts all-against-all protein alignments between the given reference genomes to infer orthologous genes. + ]]></help> + </param> + </when> + <when value="false"> </when> + </conditional> + </inputs> + <outputs> + <data name="g_embl" format="embl" label="Annotated genome in EMBL format" from_work_dir="OUT/genome.embl"/> + <data name="g_gbk" format="genbank" label="Annotated genome in GENBANK format" from_work_dir="OUT/genome.gbk"/> + <data name="g_gff" format="gff" label="Annotated genome in GFF format" from_work_dir="OUT/genome.gff"/> + <data name="e_fsa" format="fasta" label="fsa file for Genbank submission" from_work_dir="OUT/genbank/genbank.fsa"/> + <data name="e_tbl" format="txt" label="tbl file for Genbank submission" from_work_dir="OUT/genbank/genbank.tbl"/> + <data name="e_fsa" format="fasta" label="fasta file for DDBJ submission" from_work_dir="OUT/ddbj/mss.fasta"/> + <data name="e_fsa" format="txt" label="ann file for DDBJ submission" from_work_dir="OUT/ddbj/mss.ann"/> + <data name="g_fna" format="fasta" label="Genome sequences in fasta format" from_work_dir="OUT/genome.fna"/> + <data name="p_faa" format="fasta" label="Predicted proteins (fasta)" from_work_dir="OUT/protein.faa"/> + <data name="r_fna" format="fasta" label="Predicted RNAs (fasta)" from_work_dir="OUT/rna.fna"/> + <data name="c_fna" format="fasta" label="Predicted CDs (fasta)" from_work_dir="OUT/cds.fna"/> + <data name="stats" format="tabular" label="overall statistics" from_work_dir="OUT/statistics.txt"/> + </outputs> + <tests> + <test> + <param name="genome_input" value="test.genome.fna"/> + <param name="fast" value="true"/> + <param name="inputtre" value="HOG1.tre,HOG2.tre,HOG3.tre,HOG4.tre,HOG5.tre"/> + <output name="stats" file="statistics.txt"/> + </test> + </tests> + <help><![CDATA[ + DFAST is a flexible and customizable pipeline for prokaryotic genome annotation as well as data submission to the + INSDC. It is originally developed as the background engine for the DFAST web service and is also available as a + stand-alone command-line tool. + + DFAST can annotate a typical-sized bacterial genome within several minutes. In addition to the conventional + homology search, it features unique functions such as orthologous gene assignment between reference genomes, + pseudo/frameshifted gene prediction, and conserved domain search. + + This galaxy tool may be incomplete, please let us know if there is any missing functionality. + ]]></help> + <expand macro="citations" /> +</tool>