Mercurial > repos > iuc > chira_extract
diff chira_extract.xml @ 0:0a3107204741 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
author | iuc |
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date | Sun, 19 Jan 2020 16:31:03 -0500 |
parents | |
children | de66a3316735 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chira_extract.xml Sun Jan 19 16:31:03 2020 -0500 @@ -0,0 +1,130 @@ +<tool id="chira_extract" name="ChiRA extract" version="@WRAPPER_VERSION@0"> + <description>extrat the chimeras</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ + #set $genomic_fasta = '' + #if str($annotation.annot_choice) == "yes": + #if str($annotation.fasta_source.fasta_source_selector) == 'history': + #set $genomic_fasta = '$annotation.fasta_source.fasta' + #else + #set $genomic_fasta = '$annotation.fasta_source.fasta_id.fields.path' + #end if + #end if + chira_extract.py + -l '$loci' + #if str($annotation.annot_choice) == "yes": + -g '$annotation.gtf' + #if $hybridize: + -f '$genomic_fasta' + #end if + #end if + -tc '$tpm_cutoff' + -sc '$score_cutoff' + -co '$chimeric_overlap' + #if str($reference.ref_type) == "single": + -f1 '$ref_fasta' + #else if str($reference.ref_type) == "split": + -f1 '$ref_fasta1' + -f2 '$ref_fasta2' + #end if + '$hybridize' + -p "\${GALAXY_SLOTS:-2}" + -o ./ + ]]></command> + + <inputs> + <param format="tabular" name="loci" type="data" label="File containing CRLs information"/> + <conditional name="annotation"> + <param name="annot_choice" type="select" label="Have genomic information?" + help="Selecet Yes if you have an annotation file and provide corresponding genomic fasta file"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/> + <conditional name="fasta_source"> + <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file"> + <option value="history" selected="true">History</option> + <option value="preloaded">Server indexed files</option> + </param> + <when value="history"> + <param name="fasta" type="data" format="fasta" label="FASTA file" /> + </when> + <when value="preloaded"> + <param name="fasta_id" type="select"> + <options from_data_table="fasta_indexes" /> + </param> + </when> + </conditional> + </when> + <when value="no"> + <!-- Do nothing --> + </when> + </conditional> + <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1" + help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/> + <param name="score_cutoff" type="float" value="0" label="Score cut-off" min="0" max="2" + help="Hybrids with less than this score will be discarded in the final output. [0-2.0]"/> + <param name="chimeric_overlap" type="integer" value="2" + label=" Maximum number of bases allowed between the chimericsegments of a read"/> + <conditional name="reference"> + <param name="ref_type" type="select" label="Did you use single or split reference for alignment?"> + <option value="split">Split reference</option> + <option value="single">Single reference</option> + </param> + <when value="split"> + <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file" + help="Reference fasta file"/> + <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file" + help="Second reference fasta file."/> + </when> + <when value="single"> + <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file" + help="Reference fasta file"/> + </when> + </conditional> + <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" /> + </inputs> + + <outputs> + <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/> + <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/> + </outputs> + + <tests> + <test expect_num_outputs="2"> + <param name="loci" value="loci.counts"/> + <param name="ref_type" value="split"/> + <param name="ref_fasta1" value="ref1.fasta"/> + <param name="ref_fasta2" value="ref2.fasta"/> + <param name="annot_choice" value="no"/> + <param name="hybridize" value="true" /> + <output name="chimeras" file="chimeras" sort="True"/> + <output name="singletons" file="singletons" sort="True"/> + </test> + </tests> + <help> + +.. class:: infomark + +**What it does** + +This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to. + +**Inputs** + + * Tabular file containing CRLs information + * Annotation GTF file + * Reference fasta files. Provide both in case of split reference. + * If your alignments are merged at genomic level in previous step (chira merge), then provide a reference genomic fasta fille. + +**Output** + + * Tabular file containing chimeras information + </help> + <expand macro="citations" /> +</tool> +