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annotate spotyping.xml @ 2:efa2be6db310 draft default tip

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planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
author iuc
date Sun, 21 Oct 2018 13:03:00 -0400
parents f82981245fbe
children
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efa2be6db310 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
iuc
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1 <tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy2" profile="17.01">
0
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2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
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4 <macros>
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5 <import>spotyping_macros.xml</import>
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6 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">spotyping</requirement>
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10 </requirements>
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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11
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efa2be6db310 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
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12 <command detect_errors="aggressive"><![CDATA[
0
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13 #set $input_file='input.' + $input.extension
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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14 ln -s '${input}' $input_file &&
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15 SpoTyping.py
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16 $advanced.noQuery
0
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17 $advanced.seq
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18 $advanced.swift
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19 $advanced.filter
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20 $advanced.sorted
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21 $input_file &&
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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22 cat SpoTyping.log SpoTyping > '${output_txt}'
1
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23 #if $advanced.noQuery != '--noQuery':
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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24 && cp SITVIT_ONLINE.*.xls '${output_xls}'
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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25 #if $advanced.pdf_plot == 'yes':
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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26 && SpoTyping_plot.r '${output_xls}' '${output_pdf}'
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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27 #end if
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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28 #end if
0
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29 ]]>
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30 </command>
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32 <inputs>
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33 <param name="input" type="data" format="fastq,fastq.gz,fasta" label="Sequence reads" />
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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34 <section name="advanced" title="Advanced options" expanded="false">
1
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35 <param type="boolean" argument="--noQuery" label="Query SITVIT" truevalue="" falsevalue="--noQuery" checked="false" help="Query SITVIT service for report on spoligotype" />
0
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36 <param type="boolean" argument="--seq" label="Input is assembled sequence" help="Input is either a complete genomic sequence or assembled contigs from an isolate" truevalue="--seq" falsevalue="" checked="false" />
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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37 <param type="boolean" argument="--swift" label="Swift mode" checked="true" truevalue="--swift=on" falsevalue="--swift=off" />
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38 <param type="boolean" argument="--filter" label="Stringent filtering of reads" truevalue="--filter" falsevalue="" checked="false" />
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39 <param type="boolean" argument="--sorted" label="Reads are sorted to a reference genome" truevalue="--sorted" falsevalue="" />
1
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40 <param type="boolean" name="pdf_plot" label="Generate plot from SITVIT report output" truevalue="yes" falsevalue="" />
0
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41 </section>
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42 </inputs>
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43
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44 <outputs>
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45 <data name="output_txt" label="SpoTyping spoligotyping on ${on_string}" format="txt" />
1
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46 <data name="output_xls" label="SpoTyping SITVIT report on ${on_string}" format="excel.xls">
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47 <filter>advanced['noQuery']</filter>
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48 </data>
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49 <data name="output_pdf" label="SpoTyping plot from SITVIT report on ${on_string}" format="pdf">
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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50 <filter>advanced['pdf_plot']</filter>
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51 </data>
0
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52 </outputs>
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53
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54 <tests>
1
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55 <test expect_num_outputs="1">
0
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56 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
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57 <output name="output_txt">
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58 <assert_contents>
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59 <has_text text="1111111111111111101111111111111100001111111" />
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60 </assert_contents>
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61 </output>
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62 </test>
2
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63 <test expect_failure="true">
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64 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
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65 <param name="seq" value="--seq" />
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66 <assert_stderr>
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67 <has_text text="BLAST options error" />
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68 </assert_stderr>
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69 </test>
1
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70 <test expect_num_outputs="2">
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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71 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
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72 <param name="noQuery" value="" />
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73 <output name="output_txt">
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74 <assert_contents>
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75 <has_text text="1111111111111111101111111111111100001111111" />
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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76 </assert_contents>
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77 </output>
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78 <output name="output_xls">
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79 <assert_contents>
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80 <has_text text="Spoligotype" />
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81 </assert_contents>
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82 </output>
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83 </test>
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84 <test expect_num_outputs="3">
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85 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
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86 <param name="noQuery" value="" />
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87 <param name="pdf_plot" value="yes" />
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88 <output name="output_txt">
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89 <assert_contents>
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90 <has_text text="1111111111111111101111111111111100001111111" />
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91 </assert_contents>
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92 </output>
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93 <output name="output_xls">
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94 <assert_contents>
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95 <has_text text="Spoligotype" />
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96 </assert_contents>
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97 </output>
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98 <output name="output_pdf">
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99 <assert_contents>
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100 <has_text text="PDF-1.4" />
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101 </assert_contents>
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102 </output>
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103 </test>
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104
0
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105 </tests>
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106
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107 <help><![CDATA[
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108 SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs.
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109
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110 **Input:**
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111
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112 - Fastq file - if paired end data is used, you may choose to concatenate paired reads into a single input (e.g. using the cat tool)
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113 - Fasta file of a complete genomic sequence or assembled contigs of an isolate (with --seq option)
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114
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115 *Note on input size*: In swift mode the sampling threshold is reached in approximately 30x coverage when using
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116 paired end sequencing of a *M. tuberculosis* genome.
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117
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118 **Output:**
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119
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120 Count of hits from BLAST result for each spacer sequence and predicted spoligotype in the format of binary code and octal code.
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121
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122 **Options:**
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123
1
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124 \--noQuery
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125 Avoid querying the SITVIT_ online service to describe the prevalance of the reported spoligotype.
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126
0
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127 \--seq
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128 Set this if input is a fasta file that contains only complete genomic sequence or assembled contigs from an isolate. [Default is off]
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129
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130 \-s SWIFT, --swift=SWIFT
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131 Swift mode, either "on" or "off" [Default: on] - swift mode samples 250 million bases to use for spoligotyping
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132
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133 \--sorted
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134 Set if input reads are sorted relative to positions on a reference genome. If reads are sorted and swift mode is used, swift mode's sampling is adjusted
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135 to sample reads across positions in the genome evenly.
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136
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137 \--filter
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138 Filter reads such that:
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139
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140 1. Leading and trailing 'N's would be removed.
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141 2. Any read with more than 3 'N's in the middle would be removed.
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142 3. Any read with more than 7 consecutive bases identical would be trimmed/filtered out given
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143 the length of the flanking regions.
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144
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145 **Got weird spoligotype prediction?**
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146
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147 Sequencing throughput is very low (<40Mbp, for example): SpoTyping may not be able to give accurate prediction due to the relatively low read depth.
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148
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149 **Interpreting the spoligotype**
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150
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151 The binary or octal spoligotype can be used to look up lineage information using a service
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152 like `TB Lineage`_.
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153
1
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154 **SITVIT reports**
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155
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156 Optionally a report on the detected spoligotype can be retrieved from the SITVIT_ database. If such a report is requested it can also be
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157 illustrated as a (PDF format) plot.
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158
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159 .. _SpoTyping: https://github.com/xiaeryu/SpoTyping
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160 .. _spoligotype: https://www.ncbi.nlm.nih.gov/pubmed/19521871
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161 .. _TB Lineage: http://tbinsight.cs.rpi.edu/run_tb_lineage.html
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162 .. _SITVIT: http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE/
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163 ]]>
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164 </help>
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165
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166 <citations>
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167 <expand macro="spotyping_citation" />
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168 </citations>
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169 </tool>