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annotate sniffles.xml @ 0:ee65e517769d draft

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planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
author youyuh48
date Sun, 25 Aug 2019 01:58:51 -0400
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children ba3aaae7a229
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0
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1 <tool id="sniffles" name="sniffles" version="0.1.0">
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2 <description>Structural variation caller using third generation sequencing</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.11">sniffles</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 sniffles
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9 -t \${GALAXY_SLOTS:-2}
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10 -m '$input'
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11 --${output_format} '$output'
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12 ## general_options
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13 #if $general_options.s:
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14 -s $general_options.s
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15 #end if
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16 #if $general_options.max_num_splits:
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17 --max_num_splits $max_num_splits
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18 #end if
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19 #if $general_options.l:
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20 -l $general_options.l
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21 #end if
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22 #if $general_options.q:
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23 -q $general_options.q
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24 #end if
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25 #if $general_options.n:
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26 -n $general_options.n
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27 #end if
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28 #if $general_options.r:
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29 -r $general_options.r
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30 #end if
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31 ]]>
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32 </command>
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33 <inputs>
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34 <param type="data" name="input" format="bam" label="Input BAM file"/>
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35 <param name="output_format" type="select" label="Select an output format">
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36 <option value="vcf">VCF</option>
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37 <option value="bedpe">bedpe</option>
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38 </param>
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39 <section name="general_options" title="Set general options" expanded="False">
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40 <param argument="-s" type="integer" value="" optional="true" label="Minimum number of reads that support a SV. [10]"/>
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41 <param argument="--max_num_splits" name="max_num_splits" type="integer" value="" optional="true" label="Maximum number of splits per read to be still taken into account. [7]"/>
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42 <param argument="-l" type="integer" value="" optional="true" label="Minimum length of SV to be reported. [30]"/>
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43 <param argument="-q" type="integer" value="" optional="true" label="Minimum Mapping Quality. [20]"/>
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44 <param argument="-n" type="integer" value="" optional="true" label="Report up to N reads that support the SV in the vcf file. -1: report all. [0]"/>
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45 <param argument="-r" type="integer" value="" optional="true" label="Discard read if non of its segment is larger then this. [2000]"/>
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46 </section>
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47 </inputs>
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48 <outputs>
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49 <data name="output" format="vcf" label="${tool.name} on ${on_string} (${output_format} format)">
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50 <change_format>
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51 <when input="output_format" value="bedpe" format="tabular"/>
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52 </change_format>
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53 </data>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="input" value="reads_region.bam"/>
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58 <param name="option" value="--vcf"/>
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59 <output name="output" file="expected_output.vcf"/>
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60 </test>
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61 </tests>
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62 <help>
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63 <![CDATA[
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64 Usage: sniffles [options] -m <sorted.bam> -v <output.vcf>
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65
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66 Input/Output:
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67 -m <string>, --mapped_reads <string>
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68 (required) Sorted bam File
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69 -v <string>, --vcf <string>
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70 VCF output file name []
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71 -b <string>, --bedpe <string>
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72 bedpe output file name []
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73 \--Ivcf <string>
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74 Input VCF file name. Enable force calling []
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75 \--tmp_file <string>
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76 path to temporary file otherwise Sniffles will use the current directory. []
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77
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78 General:
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79 -s <int>, --min_support <int>
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80 Minimum number of reads that support a SV. [10]
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81 \--max_num_splits <int>
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82 Maximum number of splits per read to be still taken into account. [7]
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83 -d <int>, --max_distance <int>
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84 Maximum distance to group SV together. [1000]
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85 -t <int>, --threads <int>
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86 Number of threads to use. [3]
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87 -l <int>, --min_length <int>
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88 Minimum length of SV to be reported. [30]
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89 -q <int>, --minmapping_qual <int>
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90 Minimum Mapping Quality. [20]
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91 -n <int>, --num_reads_report <int>
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92 Report up to N reads that support the SV in the vcf file. -1: report all. [0]
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93 -r <int>, --min_seq_size <int>
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94 Discard read if non of its segment is larger then this. [2000]
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95 -z <int>, --min_zmw <int>
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96 Discard SV that are not supported by at least x zmws. This applies only for PacBio recognizable reads. [0]
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97 \--cs_string
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98 Enables the scan of CS string instead of Cigar and MD. [false]
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99
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100 Clustering/phasing and genotyping:
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101 \--genotype
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102 Enables Sniffles to compute the genotypes. [false]
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103 \--cluster
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104 Enables Sniffles to phase SVs that occur on the same reads [false]
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105 \--cluster_support <int>
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106 Minimum number of reads supporting clustering of SV. [1]
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107 -f <float>, --allelefreq <float>
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108 Threshold on allele frequency (0-1). [0]
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109 \--min_homo_af <float>
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110 Threshold on allele frequency (0-1). [0.8]
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111 \--min_het_af <float>
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112 Threshold on allele frequency (0-1). [0.3]
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113
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114 Advanced:
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115 \--report_BND
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116 Dont report BND instead use Tra in vcf output. [true]
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117 \--report_seq
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118 Report sequences for indels in vcf output. (Beta version!) [false]
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119 \--ignore_sd
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120 Ignores the sd based filtering. [false]
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121 \--report_read_strands
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122 Enables the report of the strand categories per read. (Beta) [false]
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123 \--ccs_reads
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124 Preset CCS Pacbio setting. (Beta) [false]
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125
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126 Parameter estimation:
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127 \--skip_parameter_estimation
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128 Enables the scan if only very few reads are present. [false]
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129 \--del_ratio <float>
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130 Estimated ration of deletions per read (0-1). [0.0458369]
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131 \--ins_ratio <float>
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132 Estimated ratio of insertions per read (0-1). [0.049379]
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133 \--max_diff_per_window <int>
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134 Maximum differences per 100bp. [50]
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135 \--max_dist_aln_events <int>
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136 Maximum distance between alignment (indel) events. [4]
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137 ]]>
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138 </help>
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139 <citations>
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140 <citation type="doi">10.1038/s41592-018-0001-7</citation>
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141 </citations>
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142 </tool>