Mercurial > repos > dfornika > tetyper
changeset 0:481b5fc3a79a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
| author | dfornika |
|---|---|
| date | Sat, 23 Nov 2019 02:35:12 +0000 |
| parents | |
| children | f38ce8ec1d87 |
| files | tetyper.xml |
| diffstat | 1 files changed, 83 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tetyper.xml Sat Nov 23 02:35:12 2019 +0000 @@ -0,0 +1,83 @@ +<tool id="tetyper" name="TETyper" version="1.1+galaxy0"> + <description></description> + <requirements> + <requirement type="package" version="1.1">tetyper</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + TETyper.py + --threads \${GALAXY_SLOTS:-1} + #if $collection_paired.selector == "paired" + --fq1 '${collection_paired.forward_input}' --fq2'${collection_paired.reverse_input}' + #elif $collection_paired.selector == "collection": + --fq1 '${single_paired.input_pair.forward}' --fq2 '${single_paired.input_pair.reverse}' + #end if + --outprefix output + ]]> + </command> + <inputs> + <conditional name="collection_paired"> + <param name="selector" type="select" label="Collection or paired reads" > + <option value="collection">Collection</option> + <option value="paired" selected="True">Paired</option> + </param> + <when value="collection"> + <param format="fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" /> + </when> + <when value="paired"> + <param format="fastq" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/> + <param format="fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/> + </when> + </conditional> + <param name="reference" /> + <param name="flank_length" /> + </inputs> + <outputs> + <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string} summary"/> + </outputs> + <tests> + </tests> + <help> + <![CDATA[ +**What it does** + +TETyper is designed for typing a specific transposable element (TE) of interest from paired-end sequencing data. It determines single nucleotide variants (SNVs) and deletions within the TE, as well as flanking sequences surrounding the TE. + +**Output** + +TETyper will produce a tab-seperated output file with the following outputs: + ++---------------+------------------------------------------------+ +| Column | Description | ++===============+================================================+ +| Deletions | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. | ++---------------+------------------------------------------------+ +| Structural_variant | | ++---------------+------------------------------------------------+ +| SNPs_homozygous | | ++---------------+------------------------------------------------+ +| SNPs_heterozygous | | ++---------------+------------------------------------------------+ +| Heterozygous_SNP_counts | | ++---------------+------------------------------------------------+ +| SNP_variant | | ++---------------+------------------------------------------------+ +| Combined_variant | | ++---------------+------------------------------------------------+ +| Left_flanks | | ++---------------+------------------------------------------------+ +| Right_flanks | | ++---------------+------------------------------------------------+ +| Left_flank_counts | | ++---------------+------------------------------------------------+ +| Right_flank_counts | | ++---------------+------------------------------------------------+ +| X_Y_presence | | ++---------------+------------------------------------------------+ + + ]]> + </help> + <citations> + <citation type="doi">10.1099/mgen.0.000232</citation> + </citations> +</tool>