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4
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1 <tool id="Resfinder" name="Resfinder" version="1">
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0
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2 <description>
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3 Resfinder: Identifcation of acquired antibiotic resistance genes
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4 </description>
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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="1.78">biopython</requirement>
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9 <requirement type="package" version="2.10.1">blast</requirement>
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10 <requirement type="package" version="1.0.8">bzip2</requirement>
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11 <requirement type="package" version="1.17.1">c-ares</requirement>
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12 <requirement type="package" version="2020.12.5">ca-certificates</requirement>
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13 <requirement type="package" version="2020.12.5">certifi</requirement>
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14 <requirement type="package" version="1.5.6">cgecore</requirement>
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15 <requirement type="package" version="7.75.0">curl</requirement>
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16 <requirement type="package" version="13.9">entrez-direct</requirement>
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17 <requirement type="package" version="2.2.10">expat</requirement>
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18 <requirement type="package" version="4.0.5">gitdb</requirement>
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19 <requirement type="package" version="3.1.14">gitpython</requirement>
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20 <requirement type="package" version="1.3.13">kma</requirement>
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21 <requirement type="package" version="1.17.2">krb5</requirement>
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22 <requirement type="package" version="2.35.1">ld_impl_linux-64</requirement>
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23 <requirement type="package" version="3.9.0">libblas</requirement>
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24 <requirement type="package" version="3.9.0">libcblas</requirement>
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25 <requirement type="package" version="7.75.0">libcurl</requirement>
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26 <requirement type="package" version="3.1.20191231">libedit</requirement>
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27 <requirement type="package" version="4.33">libev</requirement>
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28 <requirement type="package" version="3.3">libffi</requirement>
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29 <requirement type="package" version="9.3.0">libgcc-ng</requirement>
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30 <requirement type="package" version="9.3.0">libgfortran-ng</requirement>
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31 <requirement type="package" version="9.3.0">libgfortran5</requirement>
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32 <requirement type="package" version="9.3.0">libgomp</requirement>
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33 <requirement type="package" version="3.9.0">liblapack</requirement>
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34 <requirement type="package" version="1.43.0">libnghttp2</requirement>
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35 <requirement type="package" version="0.3.12">libopenblas</requirement>
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36 <requirement type="package" version="1.9.0">libssh2</requirement>
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37 <requirement type="package" version="9.3.0">libstdcxx-ng</requirement>
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38 <requirement type="package" version="6.2">ncurses</requirement>
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39 <requirement type="package" version="1.20.1">numpy</requirement>
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40 <requirement type="package" version="1.1.1">openssl</requirement>
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41 <requirement type="package" version="8.44">pcre</requirement>
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42 <requirement type="package" version="5.26.2">perl</requirement>
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43 <requirement type="package" version="1.7044">perl-app-cpanminus</requirement>
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44 <requirement type="package" version="2.32">perl-archive-tar</requirement>
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45 <requirement type="package" version="2.23">perl-base</requirement>
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46 <requirement type="package" version="3.004">perl-business-isbn</requirement>
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47 <requirement type="package" version="20140910.003">perl-business-isbn-data</requirement>
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48 <requirement type="package" version="1.38">perl-carp</requirement>
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49 <requirement type="package" version="3.74">perl-common-sense</requirement>
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50 <requirement type="package" version="2.087">perl-compress-raw-bzip2</requirement>
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51 <requirement type="package" version="2.087">perl-compress-raw-zlib</requirement>
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52 <requirement type="package" version="1.33">perl-constant</requirement>
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53 <requirement type="package" version="2.173">perl-data-dumper</requirement>
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54 <requirement type="package" version="1.03">perl-digest-hmac</requirement>
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55 <requirement type="package" version="2.55">perl-digest-md5</requirement>
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56 <requirement type="package" version="2.88">perl-encode</requirement>
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57 <requirement type="package" version="1.05">perl-encode-locale</requirement>
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58 <requirement type="package" version="5.72">perl-exporter</requirement>
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59 <requirement type="package" version="1.002001">perl-exporter-tiny</requirement>
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60 <requirement type="package" version="7.36">perl-extutils-makemaker</requirement>
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61 <requirement type="package" version="6.04">perl-file-listing</requirement>
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62 <requirement type="package" version="2.16">perl-file-path</requirement>
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63 <requirement type="package" version="0.2304">perl-file-temp</requirement>
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64 <requirement type="package" version="3.72">perl-html-parser</requirement>
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65 <requirement type="package" version="3.20">perl-html-tagset</requirement>
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66 <requirement type="package" version="5.07">perl-html-tree</requirement>
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67 <requirement type="package" version="6.04">perl-http-cookies</requirement>
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68 <requirement type="package" version="6.01">perl-http-daemon</requirement>
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69 <requirement type="package" version="6.02">perl-http-date</requirement>
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70 <requirement type="package" version="6.18">perl-http-message</requirement>
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71 <requirement type="package" version="6.01">perl-http-negotiate</requirement>
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72 <requirement type="package" version="2.087">perl-io-compress</requirement>
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73 <requirement type="package" version="1.001">perl-io-html</requirement>
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74 <requirement type="package" version="2.066">perl-io-socket-ssl</requirement>
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75 <requirement type="package" version="1.10">perl-io-zlib</requirement>
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76 <requirement type="package" version="4.02">perl-json</requirement>
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77 <requirement type="package" version="2.34">perl-json-xs</requirement>
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78 <requirement type="package" version="6.39">perl-libwww-perl</requirement>
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79 <requirement type="package" version="0.428">perl-list-moreutils</requirement>
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80 <requirement type="package" version="0.428">perl-list-moreutils-xs</requirement>
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81 <requirement type="package" version="6.04">perl-lwp-mediatypes</requirement>
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82 <requirement type="package" version="6.07">perl-lwp-protocol-https</requirement>
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83 <requirement type="package" version="3.15">perl-mime-base64</requirement>
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84 <requirement type="package" version="20180117">perl-mozilla-ca</requirement>
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85 <requirement type="package" version="6.19">perl-net-http</requirement>
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86 <requirement type="package" version="1.88">perl-net-ssleay</requirement>
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87 <requirement type="package" version="1.09">perl-ntlm</requirement>
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88 <requirement type="package" version="0.236">perl-parent</requirement>
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89 <requirement type="package" version="3.75">perl-pathtools</requirement>
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90 <requirement type="package" version="1.52">perl-scalar-list-utils</requirement>
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91 <requirement type="package" version="2.027">perl-socket</requirement>
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92 <requirement type="package" version="3.15">perl-storable</requirement>
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93 <requirement type="package" version="0.05">perl-test-requiresinternet</requirement>
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94 <requirement type="package" version="1.28">perl-time-local</requirement>
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95 <requirement type="package" version="0.30">perl-try-tiny</requirement>
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96 <requirement type="package" version="1.0">perl-types-serialiser</requirement>
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97 <requirement type="package" version="1.76">perl-uri</requirement>
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98 <requirement type="package" version="6.02">perl-www-robotrules</requirement>
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99 <requirement type="package" version="1.12">perl-xml-namespacesupport</requirement>
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100 <requirement type="package" version="2.44_01">perl-xml-parser</requirement>
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101 <requirement type="package" version="1.02">perl-xml-sax</requirement>
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102 <requirement type="package" version="1.09">perl-xml-sax-base</requirement>
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103 <requirement type="package" version="0.51">perl-xml-sax-expat</requirement>
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104 <requirement type="package" version="2.25">perl-xml-simple</requirement>
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105 <requirement type="package" version="0.24">perl-xsloader</requirement>
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106 <requirement type="package" version="21.0.1">pip</requirement>
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107 <requirement type="package" version="3.9.2">python</requirement>
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108 <requirement type="package" version="2.8.1">python-dateutil</requirement>
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109 <requirement type="package" version="3.9">python_abi</requirement>
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110 <requirement type="package" version="8.0">readline</requirement>
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111 <requirement type="package" version="49.6.0">setuptools</requirement>
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112 <requirement type="package" version="1.15.0">six</requirement>
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113 <requirement type="package" version="3.0.5">smmap</requirement>
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114 <requirement type="package" version="3.34.0">sqlite</requirement>
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115 <requirement type="package" version="0.8.9">tabulate</requirement>
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116 <requirement type="package" version="8.6.10">tk</requirement>
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117 <requirement type="package" version="2021">tzdata</requirement>
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118 <requirement type="package" version="0.36.2">wheel</requirement>
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119 <requirement type="package" version="5.2.5">xz</requirement>
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120 <requirement type="package" version="1.2.11">zlib</requirement>
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121 </requirements>
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122 <command detect_errors="exit_code"><![CDATA[
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3
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123 python3 /home/galaxy/resfinder/run_resfinder.py -s "$s" -l "$l" -t "$t" --acquired --point -ifa ${input} -db_res /home/galaxy/resfinder/db_resfinder/ -db_point /home/galaxy/resfinder/db_pointfinder/ -o output && mv ./output/ResFinder_Resistance_gene_seq.fsa $resistance_genes
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0
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124 ]]></command>
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125 <inputs>
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126 <param format="fasta" name="input" type="data" label="FASTA file : "/>
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127 <param name="s" type="select" label="Select the species:" help="*Chromosomal point mutation database exist">
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128 <option value="campylobacter">Campylobacter spp.*</option>
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129 <option value="campylobacter jejuni">Campylobacter jejuni*</option>
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130 <option value="campylobacter coli">Campylobacter coli*</option>
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131 <option value="escherichia coli">Escherichia coli*</option>
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132 <option value="salmonella">Salmonella spp.*</option>
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133 <option value="plasmodium falciparum">Plasmodium falciparum*</option>
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134 <option value="neisseria gonorrhoeae">Neisseria gonorrhoeae*</option>
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135 <option value="mycobacterium tuberculosis">Mycobacterium tuberculosis*</option>
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136 <option value="enterococcus faecalis">Enterococcus faecalis*</option>
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137 <option value="enterococcus faecium">Enterococcus faecium*</option>
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138 <option value="klebsiella">Klebsiella*</option>
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139 <option value="helicobacter pylori">Helicobacter pylori*</option>
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140 <option value="staphylococcus aureus">Staphylococcus aureus*</option>
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141 <option value="other">Other</option>
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142 </param>
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143 <param name="l" type="text" area="false" value="0.6" label="Minimum (breadth-of) coverage of ResFinder within the range 0-1:"/>
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144 <param name="t" type="text" value="0.8" area="false" label="Threshold for identity of ResFinder within the range 0-1:"/>
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145 </inputs>
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146 <outputs>
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4
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147 <collection name="outputreport" type="list" label="${tool.name} on ${on_string}: Report files">
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0
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148 <discover_datasets pattern="(?P<name>.+)\.txt$" directory="./output" format="txt"/>
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149 </collection>
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4
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150 <data format="fasta" name="resistance_genes" label="${tool.name} on ${on_string}: resistance genes"/>
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0
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151 </outputs>
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152 <help><![CDATA[
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153 This tool allows to identify acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria (in FASTA format).
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154
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155 BitBucket: https://bitbucket.org/genomicepidemiology/resfinder/src/master/
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156 ]]></help>
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157
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158 <citations>
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159 <citation type="doi">10.1093/jac/dkaa345</citation>
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160 </citations>
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161 </tool>
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