Mercurial > repos > p.lucas > clermontyping

annotate ClermonTyping_wrapper.xml @ 2:07fe3c343426 draft

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wrapper with all packages
author p.lucas
date Mon, 14 Feb 2022 14:40:43 +0000
parents cec55ef9cce5
children 01234c8a9353
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1 <tool id="ClermonTyping" name="ClermonTyping" version="1">
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2 <description>
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3 ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping
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4 </description>
2
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5 <requirements>
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6 <requirement type="package" version="0.1">_libgcc_mutex</requirement>
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7 <requirement type="package" version="4.5">_openmp_mutex</requirement>
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8 <requirement type="package" version="1.0.1">_r-mutex</requirement>
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9 <requirement type="package" version="2.35.1">binutils_impl_linux-64</requirement>
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10 <requirement type="package" version="2.35.1">binutils_linux-64</requirement>
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11 <requirement type="package" version="1.79">biopython</requirement>
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12 <requirement type="package" version="2.12.0">blast</requirement>
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14 <requirement type="package" version="1.0.8">bzip2</requirement>
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16 <requirement type="package" version="2021.10.8">ca-certificates</requirement>
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33 <requirement type="package" version="9.3.0">gfortran_linux-64</requirement>
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37 <requirement type="package" version="9.3.0">gxx_linux-64</requirement>
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104 <requirement type="package" version="3.8.12">python</requirement>
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105 <requirement type="package" version="3.8">python_abi</requirement>
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106 <requirement type="package" version="0.2.1">r-assertthat</requirement>
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110 <requirement type="package" version="4.0.5">r-bit64</requirement>
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149 <requirement type="package" version="1.2.2">r-utf8</requirement>
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150 <requirement type="package" version="0.3.8">r-vctrs</requirement>
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151 <requirement type="package" version="1.5.7">r-vroom</requirement>
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152 <requirement type="package" version="2.4.3">r-withr</requirement>
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153 <requirement type="package" version="0.29">r-xfun</requirement>
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154 <requirement type="package" version="2.2.2">r-yaml</requirement>
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155 <requirement type="package" version="8.1">readline</requirement>
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156 <requirement type="package" version="4.8">sed</requirement>
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157 <requirement type="package" version="60.8.1">setuptools</requirement>
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158 <requirement type="package" version="3.37.0">sqlite</requirement>
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159 <requirement type="package" version="2.12">sysroot_linux-64</requirement>
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160 <requirement type="package" version="8.6.11">tk</requirement>
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161 <requirement type="package" version="2.10">tktable</requirement>
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162 <requirement type="package" version="0.37.1">wheel</requirement>
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163 <requirement type="package" version="1.0.7">xorg-kbproto</requirement>
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164 <requirement type="package" version="1.0.10">xorg-libice</requirement>
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165 <requirement type="package" version="1.2.3">xorg-libsm</requirement>
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166 <requirement type="package" version="1.7.2">xorg-libx11</requirement>
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167 <requirement type="package" version="1.0.9">xorg-libxau</requirement>
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168 <requirement type="package" version="1.1.3">xorg-libxdmcp</requirement>
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169 <requirement type="package" version="1.3.4">xorg-libxext</requirement>
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170 <requirement type="package" version="0.9.10">xorg-libxrender</requirement>
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171 <requirement type="package" version="1.2.1">xorg-libxt</requirement>
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172 <requirement type="package" version="0.11.1">xorg-renderproto</requirement>
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173 <requirement type="package" version="7.3.0">xorg-xextproto</requirement>
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174 <requirement type="package" version="7.0.31">xorg-xproto</requirement>
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175 <requirement type="package" version="5.2.5">xz</requirement>
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176 <requirement type="package" version="1.2.11">zlib</requirement>
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177 <requirement type="package" version="1.5.2">zstd</requirement>
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178 </requirements>
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179 <command detect_errors="exit_code"><![CDATA[
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180 /home/galaxy/ClermonTyping/clermonTyping.sh --fasta ${input} --name Analyse
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181 ]]></command>
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182 <inputs>
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183 <param name="input" format="fasta" type="data" label="Select contigs file in fasta format." help="Fasta format containing contigs."/>
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184 </inputs>
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185 <outputs>
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186 <data name="html" format="html" label="html output file" from_work_dir="Analyse/Analyse.html"/>
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187 <data name="phylogroup" format="tsv" label="Phylogroup found" from_work_dir="Analyse/Analyse_phylogroups.txt"/>
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188 </outputs>
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189 <help>
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190 Script usage :
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191 -h : print this message and exit
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192 -v : print the version and exit
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193 --fasta : fasta contigs file(s). If multiple files, they must be separated by an arobase (@) value
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194 --name : name for this analysis (optional)
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195 --threshold : option for ClermontTyping, do not use contigs under this size (optional)
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196 --minimal : output a minimal set of files (optional)
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197 --fastafile : file with path of fasta contig file. One file by line (optional)
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198 --summary : file with path of *_phylogroups.txt. One file by line (optional)
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199 </help>
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200 </tool>