Mercurial > repos > peterjc > mira4_9_mirabait
diff tools/mira4_9/mirabait/mira4_9_mirabait.xml @ 0:c9269b5803d8 draft default tip
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
author | peterjc |
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date | Wed, 07 Oct 2015 10:31:49 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mira4_9/mirabait/mira4_9_mirabait.xml Wed Oct 07 10:31:49 2015 -0400 @@ -0,0 +1,242 @@ +<tool id="mira4_9_mirabait" name="MIRA v4.9 mirabait" version="0.0.1"> + <description>Filter reads using kmer matches</description> + <requirements> + <requirement type="binary">mirabait</requirement> + <requirement type="package" version="4.9.5">MIRA</requirement> + </requirements> + <stdio> + <!-- Assume anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <version_command interpreter="python">mira_check_version.py ${MIRA4_9}mirabait</version_command> + <command interpreter="python">./mira_check_version.py \${MIRA4_9}mirabait 4.9 && +##First checked it is mirabait v4.9 on the path... now actually run it +##----------------------------------------------------------------------- +\${MIRA4_9}mirabait -k "$kmer_length" -n "$min_occurence" -b "$bait_file" +##----------------------------------------------------------------------- +##Must now map Galaxy datatypes to MIRA file types... +##exploiting the polymorphic naming of the input read parameter! +#if $reads.filename.ext.startswith("fastq") +##MIRA doesn't like fastqsanger etc, just plain old fastq + -f fastq -t fastq +#elif $reads.filename.ext == "mira" +##We're calling *.maf the "mira" format in Galaxy (name space collision) + -f maf -t maf +#else +##MIRA is happy with fasta as name, + -f "$reads.filename.ext" -t "$reads.filename.ext" +#end if +##----------------------------------------------------------------------- +#if str($output_choice_cond.output_choice)=="both" +-o "$output_pos" -O "$output_neg" +#elif str($output_choice_cond.output_choice)=="pos" +-o "$output_pos" +#elif str($output_choice_cond.output_choice)=="neg" +-i -O "$output_neg" +#end if +##----------------------------------------------------------------------- +##Do we need to ignore the reverse strand? +#if str($strand_choice) == "fwd" +-r +#end if +##----------------------------------------------------------------------- +##Default is to mark k-mers with upper case... +#if str($output_case) == "original" +-c +#end if +##----------------------------------------------------------------------- +#if str($reads.type) == "paired" +#if $reads.filename.ext != $reads.filename2.ext +##TODO: Is there a better way to signal an error to Galaxy here? +; echo "ERROR: Paired read datatype mis-match!" ; false +#end if +-p "$reads.filename" "$reads.filename2" +#elif str($reads.type) == "interleaved" +-P "$reads.filename" +#elif str($reads.type) == "none" +"$reads.filename" +#end if + </command> + <inputs> + <!-- TODO: mirabait now allows multiple input files, and can do multiple outputs - or merge into one? --> + <!-- TODO: define a new Galaxy datatype for the bait hash file? --> + <param name="bait_file" type="data" format="fasta,fastq,mira" required="true" label="Bait file (what to look for)" /> + <conditional name="reads"> + <param name="type" type="select" label="Are these paired reads?"> + <option value="paired">Paired reads (as two files)</option> + <option value="interleaved">Paired reads (as one interleaved file)</option> + <option value="none">Unpaired reads (single or orphan reads as one file)</option> + </param> + <when value="paired"> + <param name="filename" type="data" format="fastq,fasta" required="true" label="Read file one"/> + <param name="filename2" type="data" format="fastq,fasta" required="true" label="Read file two"/> + </when> + <when value="interleaved"> + <param name="filename" type="data" format="fasta,fastq" required="true" label="Interleaved paired reads to search" /> + </when> + <when value="none"> + <param name="filename" type="data" format="fasta,fastq,mira" required="true" label="Reads to search" /> + </when> + </conditional> + <conditional name="output_choice_cond"> + <param name="output_choice" type="select" label="Output positive matches, negative matches, or both?"> + <option value="both">Both positive matches and negative matches, as two files</option> + <option value="pos" selected="true">Just positive matches, as a single file</option> + <option value="neg">Just negative matches, as a single file</option> + </param> + <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml --> + <when value="both" /> + <when value="pos" /> + <when value="neg" /> + </conditional> + <param name="output_case" type="select" label="How to use sequence case in output?"> + <option value="original">Preserve case from input</option> + <option value="bait">Mark k-mer matches in upper case</option> + </param> + <param name="strand_choice" type="select" label="Check for matches on both strands?"> + <option value="both">Check both strands</option> + <option value="fwd">Just forward strand</option> + </param> + <param name="kmer_length" type="integer" value="31" min="1" max="256" + label="k-mer length" help="Maximum 256" /> + <param name="min_occurence" type="integer" value="1" min="1" + label="Minimum k-mer occurence" + help="How many k-mer matches do you want per read? Minimum one" /> + </inputs> + <outputs> + <data name="output_pos" format_source="filename" metadata_source="filename" + label="$reads.filename.name #if str($reads.type)=='paired' then 'and $reads.filename2.name' else ''# matching $bait_file.name"> + <filter>output_choice_cond["output_choice"] != "neg"</filter> + </data> + <data name="output_neg" format_source="filename" metadata_source="filename" + label="$reads.filename.name #if str($reads.type)=='paired' then 'and $reads.filename2.name' else ''# not matching $bait_file.name"> + <filter>output_choice_cond["output_choice"] != "pos"</filter> + </data> + </outputs> + <tests> + <test> + <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> + <param name="reads|type" value="none" /> + <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" /> + <param name="output_choice" value="pos" /> + <param name="output_case" value="original" /> + <output name="output_pos" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" /> + </test> + <test> + <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> + <param name="reads|type" value="none" /> + <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" /> + <param name="output_case" value="bait" /> + <output name="output_pos" file="tvc_mini_bait_pos_case.fastq" ftype="fastqsanger" /> + </test> + <test> + <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> + <param name="reads|type" value="none" /> + <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" /> + <param name="output_case" value="bait" /> + <output name="output_pos" file="tvc_mini_bait_pos_case.fastq" ftype="fastqsanger" /> + </test> + <test> + <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> + <param name="reads|type" value="none" /> + <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" /> + <param name="output_case" value="bait" /> + <param name="kmer_length" value="32" /> + <param name="min_occurence" value="50" /> + <output name="output_pos" file="tvc_mini_bait_strict_case.fastq" ftype="fastqsanger" /> + </test> + <test> + <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> + <param name="reads|type" value="none" /> + <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" /> + <param name="output_choice" value="neg" /> + <param name="output_case" value="original" /> + <output name="output_neg" file="tvc_mini_bait_neg.fastq" ftype="fastqsanger" /> + </test> + <test> + <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> + <param name="reads|type" value="none" /> + <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" /> + <param name="output_choice" value="neg" /> + <param name="output_case" value="bait" /> + <output name="output_neg" file="tvc_mini_bait_neg_case.fastq" ftype="fastqsanger" /> + </test> + <test> + <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> + <param name="reads|type" value="none" /> + <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" /> + <param name="output_choice" value="both" /> + <param name="output_case" value="original" /> + <output name="output_pos" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" /> + <output name="output_neg" file="tvc_mini_bait_neg.fastq" ftype="fastqsanger" /> + </test> + </tests> + <help> +**What it does** + +Runs the ``mirabait`` utility from MIRA v4.9 to filter your input reads +according to whether or not they contain perfect kmer matches to your +bait file. By default this looks for 31-mers (kmers or *k*-mers where +the fragment length *k* is 31), and only requires a single matching kmer. + +The ``mirabait`` utility is useful in many applications and pipelines +outside of using the main MIRA tool for assembly or mapping. + +.. class:: warningmark + +Note ``mirabait`` cannot be used on protein (amino acid) sequences. + +**Example Usage** + +To remove over abundant entries like rRNA sequences, run ``mirabait`` with +known rRNA sequences as the bait and select the *negative* matches. + +To do targeted assembly by fishing out reads belonging to a gene and just +assemble these, run ``mirabait`` with the gene of interest as the bait and +select the *positive* matches. + +To iteratively reconstruct mitochondria you could start by fishing out reads +matching any known mitochondrial sequence, assembly those, and repeat. + + +**Notes on paired read** + +.. class:: warningmark + +Unlike ``mirabait`` from MIRA v4.0, this version is aware of paired reads +and will preserve the pairing (if either the forward or the reverse read +has enough *k*-mer matches, the pair is accepted). + + +**Citation** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999). +Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. +Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. +http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler_4_9 + </help> + <citations> + <citation type="doi">10.7717/peerj.167</citation> + <citation type="bibtex">@ARTICLE{Chevreux1999-mira3, + author = {B. Chevreux and T. Wetter and S. Suhai}, + year = {1999}, + title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information}, + journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)} + volume = {99}, + pages = {45-56}, + url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html} + }</citation> + </citations> +</tool>