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annotate tetyper.xml @ 4:ae8f5a2e723a draft

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author dfornika
date Sat, 23 Nov 2019 04:19:45 +0000
parents 9d2ddea2cde9
children 628c58844832
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1 <tool id="tetyper" name="TETyper" version="1.1+galaxy0">
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2 <description>Transposable Element Typer</description>
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3 <requirements>
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4 <requirement type="package" version="1.1">tetyper</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 TETyper.py
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9 --threads \${GALAXY_SLOTS:-1}
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10 #if $collection_paired.selector == "paired"
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11 --fq1 '${collection_paired.forward_input}' --fq2'${collection_paired.reverse_input}'
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12 #elif $collection_paired.selector == "collection":
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13 --fq1 '${collection_paired.input_pair.forward}' --fq2 '${collection_paired.input_pair.reverse}'
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14 #end if
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15 --ref '${reference}'
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16 --flank_len '${flank_length}'
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17 --outprefix output
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18 ]]>
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19 </command>
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20 <inputs>
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21 <conditional name="collection_paired">
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22 <param name="selector" type="select" label="Collection or paired reads" >
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23 <option value="collection">Collection</option>
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24 <option value="paired" selected="True">Paired</option>
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25 </param>
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26 <when value="collection">
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27 <param format="fastq,fastq.gz" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
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28 </when>
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29 <when value="paired">
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30 <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
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31 <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
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32 </when>
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33 </conditional>
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34 <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/>
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35 <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length"/>
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36 </inputs>
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37 <outputs>
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38 <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/>
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39 <data name="log" format="text" from_work_dir="output.log" label="${tool.name} on ${on_string}: log"/>
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40 </outputs>
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41 <tests>
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42 </tests>
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43 <help>
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44 <![CDATA[
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
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45 **What it does**
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46
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47 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.
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48
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49 **Output**
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51 TETyper will produce a tab-seperated output file with the following outputs:
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53 +---------------+------------------------------------------------+
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54 | Column | Description |
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55 +===============+================================================+
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56 | Deletions | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. |
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57 +---------------+------------------------------------------------+
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58 | Structural_variant | |
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59 +---------------+------------------------------------------------+
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60 | SNPs_homozygous | |
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61 +---------------+------------------------------------------------+
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62 | SNPs_heterozygous | |
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63 +---------------+------------------------------------------------+
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64 | Heterozygous_SNP_counts | |
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65 +---------------+------------------------------------------------+
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66 | SNP_variant | |
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67 +---------------+------------------------------------------------+
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68 | Combined_variant | |
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69 +---------------+------------------------------------------------+
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70 | Left_flanks | |
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71 +---------------+------------------------------------------------+
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72 | Right_flanks | |
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73 +---------------+------------------------------------------------+
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74 | Left_flank_counts | |
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75 +---------------+------------------------------------------------+
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76 | Right_flank_counts | |
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77 +---------------+------------------------------------------------+
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78 | X_Y_presence | |
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79 +---------------+------------------------------------------------+
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80
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81 ]]>
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82 </help>
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83 <citations>
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84 <citation type="doi">10.1099/mgen.0.000232</citation>
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
dfornika
parents:
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85 </citations>
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
dfornika
parents:
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86 </tool>