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annotate tetyper.xml @ 11:a97f4f1659f0 draft

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author dfornika
date Tue, 26 Nov 2019 23:27:38 +0000
parents 0291803120fc
children 3efdbbddd859
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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 '${flank_length}'
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17 --min_reads '${min_reads}'
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18 --min_each_strand '${min_each_strand}'
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19 --min_mapped_len '${min_mapped_len}'
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20 --min_qual '${min_qual}'
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21 #if $snp_profiles
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22 --snp_profiles '${snp_profiles}'
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23 #end if
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24 #if $struct_profiles
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25 --struct_profiles '${struct_profiles}'
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26 #end if
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27 --outprefix output
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28 ]]>
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29 </command>
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30 <inputs>
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31 <conditional name="collection_paired">
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32 <param name="selector" type="select" label="Collection or paired reads" >
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33 <option value="collection">Collection</option>
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34 <option value="paired" selected="True">Paired</option>
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35 </param>
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36 <when value="collection">
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37 <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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38 </when>
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39 <when value="paired">
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40 <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
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41 <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
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42 </when>
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43 </conditional>
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44 <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/>
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45 <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/>
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46 <param name="min_reads" type="integer" min="1" value="10" max="100" label="Minimum Reads" help="Minimum read number for including a specific flanking sequence."/>
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47 <param name="min_each_strand" type="integer" min="1" value="1" max="100" label="Minimum Reads (each strand)" help="Minimum read number for each strand for including a specific flanking sequence."/>
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48 <param name="min_mapped_len" type="integer" min="8" value="30" max="100" label="Minimum Mapped Length" help="Minimum length of mapping for a read to be used in determining flanking sequences. Higher values are more robust to spurious mapping. Lower values will recover more reads."/>
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49 <param name="min_qual" type="integer" min="0" value="10" max="100" label="Minimum quality" help="Minimum quality value across extracted flanking sequence." />
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50 <param name="snp_profiles" type="data" format="text" label="SNP Profiles" optional="true" />
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51 <param name="struct_profiles" type="data" format="text" label="Structural Variant Profiles" optional="true" />
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52 </inputs>
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53 <outputs>
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54 <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/>
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55 <data name="log" format="text" from_work_dir="output.log" label="${tool.name} on ${on_string}: log"/>
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="reference" value="Tn4401b-1.fasta" />
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60 <conditional name="collection_paired">
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61 <param name="selector" value="paired" />
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62 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
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63 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
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64 </conditional>
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65 <output name="summary" file="output_summary_1.txt" />
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66 </test>
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67 <test>
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68 <param name="reference" value="Tn4401b-1.fasta" />
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69 <conditional name="collection_paired">
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70 <param name="selector" value="paired" />
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71 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
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72 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
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73 </conditional>
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74 <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" />
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75 <param name="snp_profiles" value="Tn4401b_struct_profiles.txt" />
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76 <output name="summary" file="output_summary_2.txt" />
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77 </test>
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78 </tests>
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79 <help>
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80 <![CDATA[
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81 **What it does**
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83 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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84
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85 **Output**
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87 TETyper will produce a tab-seperated output file with the following outputs:
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88
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89 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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90 | Column | Description |
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91 +==========================+==================================================================================================================================================================================================================================================+
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92 | 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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93 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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94 | Structural_variant | If --struct_profiles is specified and the pattern of deletions above corresponds to one of these profiles, then the profile name is given, otherwise "unknown". |
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95 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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96 | SNPs_homozygous | A list of homozygous SNPs identified, or "none". |
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97 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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98 | SNPs_heterozygous | A list of heterozygous SNPs identified, or "none". |
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99 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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100 | Heterozygous_SNP_counts | For each heterozygous SNP, the number of reads supporting the reference and alternative calls, or "none" if there are no heterozygous SNPs. |
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101 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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102 | SNP_variant | If --snp_profiles is specified and the pattern of homozygous and heterozygous SNPs corresponds to one of these profiles, then the profile name is given. Otherwise "unknown". |
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103 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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104 | Combined_variant | Single name combining Structural_variant and SNP_variant, separated by "-". |
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105 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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106 | Left_flanks | A list of distinct sequences passing quality filters that flank the start position of the reference. |
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107 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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108 | Right_flanks | A list of distinct sequences passing quality filters that flank the end position of the reference. |
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109 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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110 | Left_flank_counts | The number of high quality reads supporting each of the left flanking sequences. |
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111 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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112 | Right_flank_counts | The number of high quality reads supporting each of the right flanking sequences. |
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113 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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114 | X_Y_presence | If --show_region is specified as --show_region X-Y, this column shows 1 if the entirety of that region is classified as present (i.e. no overlap with deleted regions), or 0 otherwise. If --show_region is unspecified, this column is omitted. |
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115 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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117 ]]>
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
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118 </help>
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
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119 <citations>
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
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120 <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
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121 </citations>
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
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122 </tool>