Mercurial > repos > rnateam > pipmir
diff pipmir.xml @ 0:16209195224c draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
author | rnateam |
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date | Fri, 25 Nov 2016 09:38:28 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pipmir.xml Fri Nov 25 09:38:28 2016 -0500 @@ -0,0 +1,252 @@ +<tool id="pipmir" name="PIPmiR PIPELINE" version="0.1.0"> + + <description>a method to identify novel plant miRNA</description> + + <requirements> + <!-- conda dependency --> + <requirement type="package" version="1.1">pipmir</requirement> + <requirement type="package" version="324">ucsc-fatotwobit</requirement> + </requirements> + + <command> +<![CDATA[ + + #if $refGenomeSource.genomeSource == "history": + faToTwoBit '$refGenomeSource.ownFile' ownFile.2bit + && + #end if + + samtools sort + + ## output in BAM format + -O BAM + + ## output file name + -o test_sorted.bam + + '$input_bam' + + && + samtools index test_sorted.bam test_sorted.bai + + ## the tool requires the location of RNAfold binary + && + RNAfold_location=\$(which RNAfold) + + && + PIPmiR PIPELINE + + -a test_sorted.bam + + ## genome source + #if $refGenomeSource.genomeSource == "history": + -t ownFile.2bit + #else + -t '$refGenomeSource.builtin.fields.path' + #end if + + -o test + + ## optional parameters + #if $params.settingsType == "custom": + ## default: 50 + -l $params.min_precursor + + ## default: 500 + -L $params.max_precursor + + ## default: 2 + -s $params.step_size + + ## default: 10 + -m $params.min_read + #end if + + ## default: 1 + -p \${GALAXY_SLOTS:-1} + + -R \$RNAfold_location + +]]> + </command> + <inputs> + <param name="input_bam" type="data" + format="sam,bam" label="Alignment" + help="The bam or sam file containing alignment of the read data."/> + + <!-- Genome source. --> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" + label="Will you select a reference genome from your + history or use a built-in genome?" + help="The version of genome against which the reads were aligned."> + <option value="2bit" selected="True"> + Use a built-in genome</option> + <option value="history"> + Use a genome from my current history</option> + </param> + <when value="2bit"> + <param name="builtin" type="select" + label="Select a reference genome"> + <options from_data_table="lastz_seqs"> + <filter type="sort_by" column="1" /> + <validator type="no_options" + message="A built-in reference genome is not available + for the build associated with the selected input file"/> + </options> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" + label="Select the reference genome" /> + </when> + </conditional> + + <!-- optional parameters --> + <conditional name="params"> + <param name="settingsType" type="select" + label="Optional parameters" + help="You can use the default settings or + set custom values for any of pipmir's parameters."> + <option value="default">Use defaults</option> + <option value="custom">Full parameter list</option> + </param> + <when value="default" /> + <!-- Full/advanced params. --> + <when value="custom"> + <param name="min_precursor" type="integer" + value="50" label="Minimum size" + help="Minimum size of a precursor sequence (Default: 50)"> + <validator type="in_range" + message="Minimum allowed value is 1" min="1"/> + </param> + + <param name="max_precursor" type="integer" + value="500" label="Maximum size" + help="Maximum size of a precursor sequence (Default: 500)"> + <validator type="in_range" + message="Minimum allowed value is 1" min="1"/> + </param> + + <param name="step_size" type="integer" + value="2" label="Step size" + help="The step size used to identifiy the precursor + from the minimum to the maximum possible + size of precursor (Default: 2)"> + <validator type="in_range" + message="Minimum allowed value is 1" min="1"/> + </param> + + <param name="min_read" type="integer" + value="10" label="Minimum read count" + help="Minimum read count for a mature to be + considered expressed (Default: 10)"> + <validator type="in_range" + message="Minimum allowed value is 1" min="1"/> + </param> + </when> <!-- full --> + </conditional> + </inputs> + <outputs> + <data name="putativeMatures" format="bed" + from_work_dir="test_putativeMatures.bed" + label="${tool.name} on ${on_string}: putative mature miRNAs"/> + + <data name="predictedPrecursors" format="txt" + from_work_dir="test_predictedPrecursors.txt" + label="${tool.name} on ${on_string}: predicted precursor"/> + + <data name="predicted_miRNA" format="txt" + from_work_dir="test_predicted_miRNAs.txt" + label="${tool.name} on ${on_string}: predicted miRNAs"/> + </outputs> + <tests> + <test> + <param name="input_bam" value="Aligned.out.sam" ftype="sam" /> + <param name="genomeSource" value="history" /> + <param name="ownFile" value="test_seq.fa" /> + <param name="settingsType" value="custom" /> + <param name="step_size" value="10" /> + <output name="putativeMatures" file="test_putativeMatures.bed" + ftype="bed"/> + <output name="predictedPrecursors" file="test_predictedPrecursors.txt" + ftype="txt"/> + <output name="predicted_miRNA" file="test_predicted_miRNAs.txt" + ftype="txt"/> + </test> + </tests> + <help> +<![CDATA[ +.. class:: infomark + +**What it does** + +`pipmir`_ is an algorithm to identify novel plant miRNA genes from a combination +of deep sequencing data and genomic features. + +.. _pipmir: https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ + +.. class:: infomark + +**Optional parameters** + +Minimum size + * The MINIMUM size the precursor predictor can search. + * 50 is recommended (and is the default). + +Maximum size + * The MAXIMUM size the precursor predictor can search. + + * The larger you make this, the longer PIPmiR will take as folding time is exponential with increased size. + + * 500 is what was used in the manuscript and will include almost all currently known Arabidopsis Thaliana miRNAs. + + * 300 is a limit that will include most known miRNAs and still have a reasonable search time. + +Step size + * The step size used to identify the precursor from the minimum to the maximum possible size of a precursor. + + * Increasing this value will speed up the precursor prediction step but limit the number of possible precursor sequences. + + * 2 is the default and is what was used in the manuscript, however 5 still works well enough, and is only slightly less accurate + +.. class:: infomark + +**Outputs** + +A `bed`_ file of putative mature miRNAs + * 'name' column = an arbitrary name given to the putative mature + * 'score' column = the read count + + .. _bed: https://genome.ucsc.edu/FAQ/FAQformat#format1 + +A text file of predicted precursors + * Form: Chromosome,Strand,Precursor_Start,Precursor_End,Sequence,Fold_Structure,Normalized_Minimum_Free_Energy,Mature_miRNA_Location + + * Chromosome = chromosome that the precursor is on + + * Strand = strand that the precursor is on + + * Precursor_Start = start nucleotide (1 based) of the precursor + + * Precursor_End = last nucleotide (1 based, inclusive) of the precursor + + * Sequence = sequence of the precursor + + * Fold_Structure = dot-bracket notation of the precursor fold centroid secondary structure (generated from RNAfold -p -d2 -noLP -noPS) + + * Normalized_Minimum_Free_Energy = minimum free energy of the centroid structure divided by the length of the sequence + + * Mature_miRNA_location = name & location of the mature miRNA within the precursor sequence + +A text file of predicted miRNAs + * This file will contain the miRNAs that had a positive classifier score, meaning that PIPmiR believes that they may be novel miRNA genes. + + * This file contains the genomic coordinates of the predicted precursor as well as for the mature and star sequences. + + * The file also contains the precursor sequence and the dot-bracket notation of its secondary structure. +]]></help> + <citations> + <citation type="doi">10.1101/gr.123547.111</citation> + </citations> +</tool>