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annotate gottcha.xml @ 3:faff3483da31 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48-dirty
author jdv
date Mon, 30 Jan 2017 20:50:49 -0500
parents dafd1d2cef8f
children 1b81bee6080f
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1 <tool id="gottcha" name="GOTTCHA" version="0.001">
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3 <description>Read-based metagenome characterization</description>
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5 <!-- ***************************************************************** -->
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7 <requirements>
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8 <requirement type="package" version="0.7.7">bwa</requirement>
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9 <requirement type="package" version="1.0b-564cf3b">gottcha</requirement>
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10 </requirements>
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12 <!-- ***************************************************************** -->
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14 <version_command>gottcha.pl -h | perl -wnE'print "$1\n" for /VERSION: (\S+)/g'</version_command>
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16 <!-- ***************************************************************** -->
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18 <command detect_errors="aggressive">
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19 <![CDATA[
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21 gottcha.pl
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23 --input '${fn_in}'
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24 --database '${db.fields.path}'
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25 --threads '\${GALAXY_SLOTS:-1}'
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26 --outdir './'
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27 --prefix results
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29 ##--General Options------------------------------
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30
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31 --relAbu ${general.rel_abund}
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32 --mode ${general.output_full}
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33 ${general.filt_plasmid}
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35 ##--Split-trim Options---------------------------
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36
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37 --minQ ${split.min_qual}
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38 --fixL ${split.fixed_len}
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39 --ascii ${split.qual_offset}
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41 ##--Filtering Options----------------------------
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43 --minCov ${filter.min_cov}
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44 --minMLHL ${filter.min_mlhl}
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45 --cCov ${filter.c_cov}
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46 --minLen ${filter.min_len}
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47 --minHits ${filter.min_hits}
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48
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49 ]]>
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50 </command>
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52 <!-- ***************************************************************** -->
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53
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54 <inputs>
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55
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56 <param name="fn_in" type="data" format="fastq" label="Input reads" help="--input" />
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57 <param name="db" type="select" label="Select a reference database" help="--database">
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58 <options from_data_table="gottcha_indices">
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59 <filter type="sort_by" column="2"/>
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60 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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61 </options>
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62 </param>
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63
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64 <section name="general" title="General Options" expanded="True">
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65 <param name="rel_abund" type="select" label="Abundance field" help="--relAbu">
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66 <option value="LINEAR_DOC" selected="true">Linear DOC</option>
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67 <option value="LINEAR_LENGTH">Linear length</option>
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68 <option value="TOTAL_BP_MAPPED">Total bp mapped</option>
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69 <option value="HIT_COUNT">Hit count</option>
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70 </param>
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71 <param name="output_full" type="boolean" truevalue="full" falsevalue="summary" checked="no" label="Output full report" help="--mode full" />
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72 <param name="filt_plasmid" type="boolean" truevalue="--noPlasmidHit" falsevalue="" checked="no" label="Filter plasmid hits" help="If true, ignore alignments to plasmids" />
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73 </section>
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74
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75 <section name="split" title="Split-trim Options" expanded="False">
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76 <param name="min_qual" size="4" type="integer" value="20" min="0" max="41" label="Minimum quality" help="Minimum quality for a read to be considered valid (0-41)" />
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77 <param name="fixed_len" size="4" type="integer" value="30" min="1" label="Trim length" help="Fixed length to which each read will be trimmed" />
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78 <param name="qual_offset" type="select" label="Quality offset" help="Base call quality offset for ASCII encoding">
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79 <option value="33" selected="true">33</option>
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80 <option value="64">64</option>
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81 </param>
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82 </section>
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83
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84 <section name="filter" title="Filtering Options" expanded="False">
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85 <param name="min_cov" size="5" type="float" value="0.005" min="0" label="Minimum coverage" help="Minimum linear coverage to be considered valid in abundance calculation" />
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86 <param name="min_mlhl" size="4" type="integer" value="5" min="0" label="Minimum MLHL" help="Minimum mean-linear-hit-length to be considered valid in abundance calculations" />
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87 <param name="c_cov" size="5" type="float" value="0.006" min="0" label="Critical coverage for MLHL" help="Critical coverage below which Minimum MLHL will cause an organism to fail" />
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88 <param name="min_len" size="4" type="integer" value="100" min="0" label="Minimum length" help="Minimum unique length to be considered valid in abundance calculation" />
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89 <param name="min_hits" size="4" type="integer" value="10" min="0" label="Minimum hits" help="Minimum number of hits to be considered valid in abundance calculation" />
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90 </section>
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91
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92 </inputs>
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93
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94 <!-- ***************************************************************** -->
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95
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96 <outputs>
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97
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98 <data name="out_log" format="txt" label="GOTTCHA on ${on_string}: Log" from_work_dir="results.gottcha.log" />
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99 <data name="out_tsv" format="txt" label="GOTTCHA on ${on_string}: Summary" from_work_dir="results.gottcha.tsv" />
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100 <data name="out_full" format="txt" label="GOTTCHA on ${on_string}: Full Report" from_work_dir="results.gottcha_full.tsv">
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101 <filter>output_full</filter>
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102 </data>
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103
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104 </outputs>
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105
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106 <!-- ***************************************************************** -->
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107
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108 <tests>
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109 <test>
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110 <param name="db" value="test_db" />
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111 <param name="fn_in" ftype="fastq" value="test.fq" />
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112 <param name="output_full" value="no" />
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113 <param name="min_hits" value="1" />
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114 <output name="out_tsv" file="test_02.tsv" />
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115 <output name="out_log" file="test_02.log" compare="sim_size" delta="2000"/>
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116 </test>
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117 </tests>
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118
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119 <!-- ***************************************************************** -->
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120
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121 <help>
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122 <![CDATA[
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123
1
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124 **Description**
0
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125
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126 Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) is an
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127 annotation-independent and signature-based metagenomic taxonomic profiling
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128 tool that has significantly smaller FDR than other profiling tools. This Perl
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129 script is a wrapper to run the GOTTCHA profiling tool with pre-computed
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130 signature databases. The procedure includes 3 major steps: split-trimming the
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131 input data, mapping reads to a GOTTCHA database using BWA, profiling/filtering
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132 the result.
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133
1
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134 **Options**
0
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135 ::
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136
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137 --relAbu|r <STRING> The field will be used to calculate relative
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138 abundance. You can specify one of the following
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139 fields: "LINEAR_LENGTH", "TOTAL_BP_MAPPED",
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140 "HIT_COUNT", "LINEAR_DOC".
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141 [default: LINEAR_DOC]
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142 --mode|m <STRING> You can specify one of the output mode:
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143 "summary" : this mode will report a summary of
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144 profiling result to *.gottcha.tsv file.
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145 "full" : other than a summary, this mode will
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146 report unfiltered result to
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147 *.gottcha_full.tsv with more detail.
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148 "all" : other than two tables, this mode will
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149 keep all output files that were
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150 generated by each profiling step.
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151 [default: summary]
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152 --noPlasmidHit|n Ignore alignments that hit to plasmids
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153 [default: null]
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154
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155 *** OPTIONS FOR SPLIT-TRIMMING READS ***
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156
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157 --minQ <INT> Minimum quality for a read to be considered valid
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158 (0-41) [default: 20]
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159 --fixL <INT> Fixed length to which each trimmed read will be cut
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160 down to [default: 30]
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161 --ascii <INT> ASCII encoding of quality score (33 or 64) [default:
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162 33]
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163
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164 *** OPTIONS FOR FILTERING PROFILING RESULT ***
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165
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166 --minCov <FLOAT> Minimum linear coverage to be considered valid in
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167 abundance calculation [default: 0.005]
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168 --minMLHL <INT> Minimum Mean-Linear-Hit-Length to be considered valid
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169 in abundance calculation [default: 5]
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170 --cCov <FLOAT> Critical coverage below which --minMLHL will cause an
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171 organism to fail [default: 0.006]
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172 --minLen <INT> Minimum unique length to be considered valid in
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173 abundance calculation [default: 100]
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174 --minHits <INT> Minimum number of hits to be considered valid in
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175 abundance calculation [10]
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176
1
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177 **Interpreting Results**
0
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178
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179 GOTTCHA reports profiling results in a neat summary table
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180 by default. The tsv file will list the organism(s) at all taxonomic
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181 levels from STRAIN to PHYLUM, their linear length, total bases mapped,
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182 linear depth of coverage, and the normalized linear depth of coverage. The
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183 linear depth of coverage (LINEAR_DOC) is used to calculate relative
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184 abundance of each organism or taxonomic name in the sample.
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185
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186 Summary table:
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187
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188 ================= ==============================
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189 Column Description
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190 ================= ==============================
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191 LEVEL taxonomic rank
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192 NAME taxonomic name
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193 REL_ABUNDANCE relative abundance (equivalent to NORM_COV by default)
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194 LINEAR_LENGTH number of non-overlapping bases covering the signatures
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195 TOTAL_BP_MAPPED sum total of all hit lengths recruited to signatures
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196 HIT_COUNT number of hits recruited to signatures
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197 HIT_COUNT_PLASMID number of hits recruited to signatures
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198 READ_COUNT number of reads recruited to signatures
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199 LINEAR_DOC linear depth-of-coverage (TOTAL_BP_MAPPED / LINEAR_LENGTH)
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200 NORM_COV normalized linear depth-of-coverage (LINEAR_DOC / SUM(LINEAR_DOC in certain level))
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201 ================= ==============================
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202
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203 Other than a summary table, "full" report mode will report a table with more
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204 detail information from unfiltered results. The explanation of each column in
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205 the full report is as follows:
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206
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207 ================================== ==========================
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208 Column Description
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209 ================================== ==========================
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210 RANKNAME (REPLICON) = replicon name (source + plasmid/chr)<br>(STRAIN) = strain name<br>(SPECIES) = species name<br>(GENUS) = genus name<br>...
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211 NUM_SUBRANKS no. of distinct subranks for the current rank<br>(E.g. the no. of SPECIES under the current GENUS)
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212 GPROJ_ENTRIES no. of genome projects (i.e. STRAINS) under this RANK NAME
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213 LINEAR_LENGTH N/O_LENGTH<br>= non-overlapping length <br>= no. of non-overlapping bases covering the unique DB
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214 UNIQUE_DB_LENGTH no. of unique bases for this organism
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215 FULL_REFDB_LENGTH no. of bases in full reference
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216 LINEAR_COV LINEAR_LENGTH / UNIQUE_DB_LENGTH
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217 HIT_COUNT no. of hits recruited to genome
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218 HIT_COUNT_PLASMID no. of hits recruited to plasmid
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219 READ_COUNT no. of reads recruited to genome
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220 FULL_HIT_COUNT no. of full-length read hits recruited to genome
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221 TOTAL_BP_MAPPED sum total of all hit lengths recruited to genome<br>= hit1.length + hit2.length + ... hitX.length<br>[formerly FOLD_COV_UNIQUE_SAMPLE]
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222 LINEAR_DOC linear depth-of-coverage<br>= fold coverage of sample's LINEAR_LENGTH <br>= TOTAL_BP_MAPPED / LINEAR_LENGTH<br>[formerly FOLD_COV_UNIQUE_REFDB]
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223 UREF_DOC unique reference's depth-of-coverage<br>= fold coverage of reference's UNIQUE_DB_LENGTH<br>= TOTAL_BP_MAPPED / UNIQUE_DB_LENGTH
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224 UREF_CMAX MAX COVERAGE OF REFDB POSSIBLE, GIVEN SAMPLE INPUT BASES<br>= Cmax = L0/l0 <br>= TOTAL_INPUT_BASES / UNIQUE_DB_LENGTH
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225 FRAC_HITS_POSSIBLE HIT_COUNT / TOTAL_INPUT_READS
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226 FRAC_BASES_POSSIBLE TOTAL_BP_MAPPED / TOTAL_INPUT_BASES
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227 MEAN_HIT_LENGTH TOTAL_BP_MAPPED / HIT_COUNT
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228 MEAN_LINEAR_HIT_LENGTH LINEAR_LENGTH / HIT_COUNT
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229 best_SUBRANK name of the best subrank (determined by the highest LINEAR_COV)
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230 best_NUM_SUBRANKS no. of subranks supporting current "SUBRANK"<br>{SS} = no. of GI entries supporting this strain<br>{S} = no. of strains supporting this species<br>{G} = no. of species supporting this genus<br>{F} = no. of genera supporting this family<br>{O} = no. of families supporting this order <br>{C} = no. of orders supporting this class<br>{P} = no. of classes supporting this phylum
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231 best_GPROJ_ENTRIES no. of genome projects (i.e. STRAINS) under this best_SUBRANK<br>{SS} = no. of genome projects supporting this strain = 1<br>{S} = no. of genome projects supporting this species<br>{G} = no. of genome projects supporting this genus<br>{F} = no. of genome projects supporting this family<br>{O} = no. of genome projects supporting this order<br>{C} = no. of genome projects supporting this class<br>{P} = no. of genome projects supporting this phylum
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232 best_LINEAR_LENGTH
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233 best_UNIQUE_DB_LENGTH
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234 best_FULL_REFDB_LENGTH
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235 best_LINEAR_COV
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236 best_HIT_COUNT
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237 best_FULL_HIT_COUNT
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238 best_TOTAL_BP_MAPPED
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239 best_LINEAR_DOC (a.k.a. Abundance)
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240 best_UREF_DOC
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241 best_UREF_CMAX
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242 best_FRAC_HITS_POSSIBLE
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243 best_FRAC_BASES_POSSIBLE
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244 best_MEAN_HIT_LENGTH
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245 best_MEAN_LINEAR_HIT_LENGTH
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246 CONTIG_COUNT no. of contiguous fragments<br> (after mapping & generating non-overlapping fragments)
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247 CONTIG_MEAN_LEN mean length of contigs (bp)
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248 CONTIG_STDEV_LEN standard deviation of contig lengths (bp)
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249 CONTIG_MINLEN length of smallest contig
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250 CONTIG_MAXLEN length of largest contig
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251 CONTIG_HISTOGRAM(LEN:FREQ) contig Length Histogram<br> (in the format contigLength:frequency)
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252 ================================== ==========================
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253
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254 ]]>
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255 </help>
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256
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257 <!-- ***************************************************************** -->
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258
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259 <citations>
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260 <citation type="doi">10.1093/nar/gkv180</citation>
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261 </citations>
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262
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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263 </tool>