Mercurial > repos > smarthey > paqmir_mirdeep2_quantifier
diff paqmir_quantifier/quantifier.xml @ 0:bf20f97162f7 draft default tip
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| author | smarthey |
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| date | Mon, 18 Mar 2019 09:36:28 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paqmir_quantifier/quantifier.xml Mon Mar 18 09:36:28 2019 -0400 @@ -0,0 +1,198 @@ +<tool id="paqmir_mirdeep2_quantifier" name="PAQmiR MiRDeep2 Quantifier" version="2.1.0"> + <description>fast quantitation of reads mapping to known miRBase precursors</description> + <requirements> + <requirement type="package" version="2.0.0.8">mirdeep2</requirement> + </requirements> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + <command> +<![CDATA[ +#import subprocess +#set $mature_file = $subprocess.check_output(["basename",$mature.file_name]) +#set $mature_file = $mature_file.rstrip() + quantifier.pl + + -p $precursors + + -m $mature + + -r $reads + + #if $species.value != 'all' + -t $species + #end if + + #if $option.choice + + #if $option.star_sequences + -s $option.star_sequences + #end if + + $option.sortReadsInPDF + $option.flexibleIdMapping + $option.skipFileConversion + $option.wholePrecursAsMature + $option.discardReadMultiMap + + -e $option.upstreamNtides + -f $option.downstreamNtides + -g $option.allowedMismatches + + $option.identifiers_supv18 + + #end if + + -y galaxy + + ## html output + ; + cp expression_galaxy.html $html 2> /dev/null + + ## move pdf directory to be accessible from the new index.html + ; + mkdir -p $html.files_path 2> /dev/null + ; + cp -R pdfs_galaxy $html.files_path 2> /dev/null + ; + cp expression_analyses/expression_analyses_galaxy/${mature_file}_mapped.arf expression_analyses/expression_analyses_galaxy/mature_mapped.arf + ]]> + </command> + <inputs> + <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads" help="Reads in fasta format. (-r)"/> + <param name="precursors" format="fasta" type="data" label="Precursor sequences" help="miRNA precursor sequences from miRBase. (-p)"/> + <param name="mature" format="fasta" type="data" label="Mature miRNA sequences" help="Mature miRNA sequences from miRBase. (-m)"/> + <param name="species" type="select" label="Search in species" help="If not searching in a specific species all species in your files will be analyzed. (-t) [ If you don't find the specie you need you can use 'All species' or contact the administrator to update the list ] "> + <option value="all">All species</option> + <option value="hsa">Human</option> + <option value="ptr">Chimp</option> + <option value="na">Orangutan</option> + <option value="na">Rhesus</option> + <option value="na">Marmoset</option> + <option value="mmu">Mouse</option> + <option value="rno">Rat</option> + <option value="na">GuineaPig</option> + <option value="lca">Cat</option> + <option value="cfa">Dog</option> + <option value="eca">Horse</option> + <option value="bta">Cow</option> + <option value="na">Opossum</option> + <option value="na">Platypus</option> + <option value="gga">Chicken</option> + <option value="na">Zebrafinch</option> + <option value="na">Lizard</option> + <option value="xtr">X.tropicalis</option> + <option value="dre">Zebrafish</option> + <option value="tni">Tetraodon</option> + <option value="fru">Fugu</option> + <option value="na">Stickleback</option> + <option value="na">Medaka</option> + <option value="na">Lamprey</option> + <option value="bfl">Lancelet</option> + <option value="cin">C.intestinalis</option> + <option value="spu">S.purpuratus</option> + <option value="cel">C.elegans</option> + <option value="na">C.brenneri</option> + <option value="cbr">C.briggsae</option> + <option value="na">C.remanei</option> + <option value="sja">C.japonica</option> + <option value="na">P.pacificus</option> + <option value="dme">D.melanogaster</option> + <option value="dsi">D.simulans</option> + <option value="dse">D.sechellia</option> + <option value="dya">D.yakuba</option> + <option value="der">D.erecta</option> + <option value="dan">D.ananassae</option> + <option value="dps">D.pseudoobscura</option> + <option value="dpe">D.persimilis</option> + <option value="dvi">D.virilis</option> + <option value="dmo">D.mojavensis</option> + <option value="dgr">D.grimshawi</option> + <option value="aga">A.gambiae</option> + <option value="ame">A.mellifera</option> + <option value="na">S.cerevisiae</option> + <option value="cel">Worm</option> + </param> + + <conditional name="option"> + <param name="choice" type="boolean" truevalue="yes" falsevalue="no" label="More options?"/> + <when value="no"> + </when> + <when value="yes"> + <param name="identifiers_supv18" type="boolean" truevalue="-P" falsevalue="" label="Mature miRNA reference contain miRBase v>=18 identifiers" help="Use this switch if Mature miRNA reference contain miRBase v18 (or more recent) identifiers (5p and 3p) instead of previous ids from v17. (-P)"/> + <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/> + <!-- <param name="generatePDFs" type="boolean" checked="true" truevalue="" falsevalue="-d" label="Generate PDFs" help="(-d)"/> --> + <param name="sortReadsInPDF" type="boolean" checked="true" truevalue="" falsevalue="-o" label="Sort reads by sample in PDF" help="(-o)"/> + <param name="flexibleIdMapping" type="boolean" checked="false" truevalue="-k" falsevalue="" label="Include ID-flexible mapping" help="Also considers precursor-mature mappings that have different ids, eg let7c would be allowed to map to pre-let7a. (-k)"/> + <param name="skipFileConversion" type="boolean" checked="false" truevalue="-n" falsevalue="" label="Skip file conversion" help="(-n)"/> + <param name="skipPrecursMapping" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Skip mapping against precursor" help="(-x)"/> + <!-- <param name="noMrdPDF" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Do not create output.mrd file or PDFs" help="(-j)"/> --> + <param name="wholePrecursAsMature" type="boolean" checked="false" truevalue="-w" falsevalue="" label="Consider the whole precursor as the 'mature sequence'" help="(-w)"/> + <param name="discardReadMultiMap" type="boolean" checked="false" truevalue="-U" falsevalue="" label="Discard all read multimapper" help="(-U)"/> + + <param name="upstreamNtides" type="integer" value="2" min="0" label="Upstream nucleotides" help="Number of nucleotides upstream of the mature sequence to consider. (-e)"/> + <param name="downstreamNtides" type="integer" value="5" min="0" label="Downstream nucleotides" help="Number of nucleotides downstream of the mature sequence to consider. (-f)"/> + <param name="allowedMismatches" type="integer" value="1" min="0" label="Allowed mismatches" help="Number of allowed mismatches when mapping reads to precursors. (-g)"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="miRNAsExpressed" format="tabular" from_work_dir="miRNAs_expressed_all_samples_galaxy.csv" label="output of ${tool.name} on ${on_string}"/> + <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"/> + <data name="miRBase" format="tabular" from_work_dir="expression_analyses/expression_analyses_galaxy/miRBase.mrd" label="miRBase.mrd of ${tool.name} on ${on_string}"/> + <data name="mature_and_new_mapped" format="tabular" from_work_dir="expression_analyses/expression_analyses_galaxy/mature_mapped.arf" label="${mature.name}_mapped.arf of ${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="reads" value="reads_collapsed.fa"/> + <param name="precursors" value="precursors_ref_this_species.fa"/> + <param name="mature" value="mature_ref_this_species.fa"/> + <param name="species" value="cel"/> + <output name="miRNAsExpressed" file="miRNAs_expressed_all_samples.csv"/> + <output name="html" file="expression_galaxy.html"/> + </test> + </tests> + <help> +<![CDATA[ + + | This tool is part of the workflow **PAQmiR** for the *Prediction Annotation and Quantification of miRNA with miRDeep2* + | + | *This wrapper was forked from the rbc_mirdeep2_quantifier wrapper of the RNA-Bioinformatics network* + | ==> https://www.denbi.de/network/rna-bioinformatics-center-rbc + | ==> https://github.com/bgruening + | + | Modifications are the product of Valentin Marcon & Sylvain Marthey (Thanks to INRA Migale, IFB ressources & INRA GABI) + +**What it does** + + | The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. + | First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. + | By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. + | The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined. + +**Input** + +A FASTA file with precursor sequences, a FASTA file with mature miRNA sequences, a FASTA file with deep sequencing reads and optionally a FASTA file with star sequences and the 3 letter code of the species of interest. + +**Output** + +A tab separated file with miRNA identifiers and its read count, a signature file, a html file that gives an overview of all miRNAs the input data and a pdfs that contains for each miRNA a pdf file showing its signature and structure. + +**Dependency** + +MiRDeep2_ 2.0.0.8, Conda version + +.. _mirdeep2: https://anaconda.org/bioconda/mirdeep2 + +]]> + </help> + <citations> + <citation type="doi">10.1093/nar/gkr688</citation> + <citation type="doi">10.1002/0471250953.bi1210s36</citation> + </citations> +</tool>