Mercurial > repos > iuc > kofamscan

annotate kofamscan.xml @ 4:2eb7932e91a3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 431ba943dcd0a584a64f28924396f3508c84f6b9
author iuc
date Thu, 25 Apr 2024 20:57:51 +0000
parents c3c46f14c7a4
children 8ec7636fa875
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4
2eb7932e91a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 431ba943dcd0a584a64f28924396f3508c84f6b9
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1 <tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
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2 <description>gene function annotation based on KEGG orthology and HMM</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.3.0</token>
4
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5 <token name="@VERSION_SUFFIX@">3</token>
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6 <xml name="reportannotation" token_selected="">
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7 <param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/>
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8 </xml>
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9 </macros>
2
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10 <xrefs>
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11 <xref type="bio.tools">kofamscan</xref>
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12 </xrefs>
0
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13 <requirements>
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14 <requirement type="package" version="@TOOL_VERSION@">kofamscan</requirement>
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15 <requirement type="package" version="3.0">zip</requirement>
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16 </requirements>
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17 <version_command><![CDATA[exec_annotation --version | cut -d " " -f 2]]></version_command>
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18 <command detect_errors="exit_code"><![CDATA[
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19 #if $p_cond.p_sel != "cached"
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20 ## preprocessing
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21 mkdir ./profile &&
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22 mkdir ./temp_extract &&
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23 #if $p_cond.p_sel == 'compressed'
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24 tar -xf '${p_cond.p}' -C temp_extract &&
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25 find ./temp_extract/ -name '*.hmm' -exec mv {} ./profile \; &&
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26 find ./temp_extract/ -name '*.hal' -exec mv {} ./profile \; &&
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27 #elif $p_cond.p_sel == 'hmm'
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28 ## input files require prefix 'K' and file extension '.hmm'
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29 #for $i, $current in enumerate($p_cond.p)
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30 ln -s '$current' 'profile/K${i}.hmm' &&
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31 #end for
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32 #end if
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33 #end if
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34
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35 ## run
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36 exec_annotation
3
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37
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38 #if $p_cond.p_sel != "cached"
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39 -p 'profile'
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40 -k '$p_cond.k'
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41 #else
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42 -p '$p_cond.kofam.fields.profile_dir/#if $p_cond.kofam_subset then $p_cond.kofam_subset else ""#'
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43 -k '$p_cond.kofam.fields.ko_list'
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44 #end if
0
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45 -o 'result.txt'
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46 --cpu \${GALAXY_SLOTS:-4}
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47 -E $E
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48 -T $ap.T
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49 -f '$ap.f_cond.f_sel'
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50 $ap.f_cond.reportannotation
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51 #if 'alignments' in $ap.out
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52 --create-alignment
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53 #end if
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54 '$query'
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55
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56 ## postprocessing
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57 #if 'alignments' in $ap.out
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58 && test -d 'tmp/alignment' && zip -q -r 'tmp/alignments.zip' tmp/alignment/* || echo 'No alignment files.'
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59 #end if
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60 ]]></command>
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61 <inputs>
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62 <param name="query" type="data" format="fasta" label="Select query sequence file" help="Nucleotide sequences are not accepted."/>
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63 <conditional name="p_cond">
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64 <param name="p_sel" type="select" label="Select profile database format">
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65 <option value="cached" selected="true">Cached</option>
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66 <option value="compressed">Compressed set of HMM and HAL file(s)</option>
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67 <option value="hmm">HMM file(s)</option>
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68 </param>
3
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69 <when value="cached">
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70 <param name="kofam" type="select">
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71 <options from_data_table="kofam"/>
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72 </param>
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73 <param name="kofam_subset" type="select" optional="true">
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74 <options from_data_table="kofam_subset">
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75 <filter type="param_value" column="2" ref="kofam"/>
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76 <filter type="sort_by" column="1"/>
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77 <filter type="unique_value" column="1"/>
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78 <column name="name" index="1"/>
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79 <column name="value" index="0"/>
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80 </options>
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81 <validator type="no_options" message="No option available for this input"/>
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82 </param>
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83 </when>
0
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84 <when value="compressed">
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85 <param argument="-p" type="data" format="tar" label="Select a compressed file with HMM and HAL file(s)" help="Compressed archives are available from KofamKOALA web service (https://www.genome.jp/tools/kofamkoala/)."/>
3
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86 <param argument="-k" type="data" format="tabular" label="Select KO list file"/>
0
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87 </when>
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88 <when value="hmm">
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89 <param argument="-p" type="data" format="hmm3" multiple="true" label="Select profile HMM file(s)"/>
3
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90 <param argument="-k" type="data" format="tabular" label="Select KO list file"/>
0
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91 </when>
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92 </conditional>
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93 <param argument="-E" type="float" min="0.0" max="1.0" value="0.01" label="Set E-value threshold"/>
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94 <section name="ap" title="Advanced parameters" expanded="true">
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95 <param argument="-T" type="integer" value="1" label="Set threshold scale" help="The score thresholds will be multiplied by this value."/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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96 <conditional name="f_cond">
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97 <param name="f_sel" type="select" label="Select output format">
4
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98 <option value="detail">Details for each hit (including hits below threshold) (detail)</option>
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99 <option value="detail-tsv" selected="true">Tab separeted values for detail format (detail-tsv)</option>
0
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100 <option value="mapper">KEGG Mapper compatible format (mapper)</option>
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101 <option value="mapper-one-line">KEGG Mapper compatible format, but all hit KOs are listed in one line (mapper-oneline)</option>
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102 </param>
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103 <when value="detail">
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104 <expand macro="reportannotation" selected="false"/>
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105 </when>
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106 <when value="detail-tsv">
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107 <expand macro="reportannotation" selected="false"/>
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108 </when>
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109 <when value="mapper">
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110 <expand macro="reportannotation" selected="true"/>
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111 </when>
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112 <when value="mapper-one-line">
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113 <expand macro="reportannotation" selected="true"/>
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114 </when>
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115 </conditional>
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116 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Only shown in history if selected here and generated by the specific run.">
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117 <option value="result" selected="true">KofamScan Result</option>
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118 <option value="alignments">HMMER alignments</option>
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119 <option value="output">HMMER run output</option>
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120 <option value="tabular">HMMER tabular summary</option>
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121 </param>
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122 </section>
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123 </inputs>
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124 <outputs>
3
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125 <data name="out_result" format="txt" from_work_dir="result.txt" label="${tool.name} on ${on_string}: Results">
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126 <filter>'result' in ap['out']</filter>
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127 <change_format>
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128 <when input='ap.f_cond.f_sel' value="detail-tsv" format="tabular" />
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
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129 </change_format>
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130 </data>
0
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131 <data name="out_alignments" format="zip" from_work_dir="tmp/alignments.zip" label="${tool.name} on ${on_string}: HMMER alignments">
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132 <filter>'alignments' in ap['out']</filter>
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133 </data>
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134 <data name="out_output" format="txt" from_work_dir="tmp/output/output.txt" label="${tool.name} on ${on_string}: HMMER output">
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135 <filter>'output' in ap['out']</filter>
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136 </data>
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137 <data name="out_tabular" format="txt" from_work_dir="tmp/tabular/tabular.txt" label="${tool.name} on ${on_string}: HMMER tabular">
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138 <filter>'tabular' in ap['out']</filter>
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139 </data>
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140 </outputs>
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141 <tests>
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142 <!-- #1 default -->
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143 <test expect_num_outputs="1">
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144 <param name="query" value="query.fasta"/>
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145 <conditional name="p_cond">
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146 <param name="p_sel" value="compressed"/>
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147 <param name="p" value="profiles.tar.gz"/>
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148 </conditional>
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149 <param name="k" value="ko"/>
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150 <output name="out_result">
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151 <assert_contents>
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152 <has_n_lines n="5"/>
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153 <has_text_matching expression=".+sp\|P00329\|ADH1_MOUSE.+"/>
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154 </assert_contents>
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155 </output>
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156 </test>
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157 <!-- #2 -->
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158 <test expect_num_outputs="4">
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159 <param name="query" value="query.fasta"/>
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160 <conditional name="p_cond">
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161 <param name="p_sel" value="hmm"/>
3
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162 <param name="p" value="profiles/K00001.hmm,profiles/K00002.hmm,profiles/K00003.hmm"/>
0
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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163 </conditional>
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164 <param name="k" value="ko"/>
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165 <param name="E" value="0.02"/>
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166 <section name="ap">
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167 <param name="T" value="2"/>
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168 <conditional name="f_cond">
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169 <param name="f_sel" value="detail-tsv"/>
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170 <param name="reportannotation" value="true"/>
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171 </conditional>
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172 <param name="out" value="alignments,output,result,tabular"/>
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173 </section>
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diff changeset
174 <output name="out_alignments">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
175 <assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
176 <has_size value="4099"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
177 </assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
178 </output>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
179 <output name="out_output">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
180 <assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
181 <has_n_lines n="224"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
182 <has_line line="Internal pipeline statistics summary:"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
183 </assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
184 </output>
3
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
185 <output name="out_result" ftype="tabular">
0
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
186 <assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
187 <has_n_lines n="9"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
188 <has_text_matching expression=".+sp\|P19858\|LDHA_BOVIN"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
189 </assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
190 </output>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
191 <output name="out_tabular">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
192 <assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
193 <has_n_lines n="48"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
194 <has_line line="K1"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
195 </assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
196 </output>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
197 </test>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
198 <!-- #3 -->
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
199 <test expect_num_outputs="1">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
200 <param name="query" value="query.fasta"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
201 <conditional name="p_cond">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
202 <param name="p_sel" value="hmm"/>
3
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
203 <param name="p" value="profiles/K00001.hmm,profiles/K00002.hmm,profiles/K00003.hmm"/>
0
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
204 </conditional>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
205 <param name="k" value="ko"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
206 <section name="ap">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
207 <conditional name="f_cond">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
208 <param name="f_sel" value="mapper"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
209 </conditional>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
210 </section>
3
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
211 <output name="out_result" ftype="txt">
0
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
212 <assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
213 <has_n_lines n="7"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
214 <has_line line="sp|P19858|LDHA_BOVIN"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
215 </assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
216 </output>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
217 </test>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
218 <!-- #4 -->
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
219 <test expect_num_outputs="1">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
220 <param name="query" value="query.fasta"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
221 <conditional name="p_cond">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
222 <param name="p_sel" value="hmm"/>
3
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
223 <param name="p" value="profiles/K00001.hmm,profiles/K00002.hmm,profiles/K00003.hmm"/>
0
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
224 </conditional>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
225 <param name="k" value="ko"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
226 <section name="ap">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
227 <conditional name="f_cond">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
228 <param name="f_sel" value="mapper-one-line"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
229 </conditional>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
230 </section>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
231 <output name="out_result">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
232 <assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
233 <has_n_lines n="7"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
234 <has_line line="sp|P19858|LDHA_BOVIN"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
235 </assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
236 </output>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
237 </test>
1
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
238 <!-- #5 -->
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
239 <test expect_num_outputs="1">
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
240 <param name="query" value="query.fasta"/>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
241 <conditional name="p_cond">
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
242 <param name="p_sel" value="compressed"/>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
243 <param name="p" value="profilesTyp2.tar.gz"/>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
244 </conditional>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
245 <param name="k" value="ko"/>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
246 <output name="out_result">
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
247 <assert_contents>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
248 <has_n_lines n="5"/>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
249 <has_text_matching expression=".+sp\|P00329\|ADH1_MOUSE.+"/>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
250 </assert_contents>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
251 </output>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
252 </test>
3
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
253 <!-- #6 test with cached data -->
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
254 <test expect_num_outputs="1">
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
255 <param name="query" value="query.fasta"/>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
256 <conditional name="p_cond">
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
257 <param name="p_sel" value="cached"/>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
258 <param name="kofam" value="test_value"/>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
259 </conditional>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
260 <param name="k" value="ko"/>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
261 <section name="ap">
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
262 <conditional name="f_cond">
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
263 <param name="f_sel" value="mapper-one-line"/>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
264 </conditional>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
parents: 2
diff changeset
265 </section>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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266 <output name="out_result" ftype="txt">
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267 <assert_contents>
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268 <has_n_lines n="7"/>
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269 <has_line line="sp|P19858|LDHA_BOVIN"/>
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270 </assert_contents>
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271 </output>
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272 </test>
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273 <!-- #6 test with cached data + subset -->
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274 <test expect_num_outputs="1">
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275 <param name="query" value="query.fasta"/>
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276 <conditional name="p_cond">
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277 <param name="p_sel" value="cached"/>
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278 <param name="kofam" value="test_value"/>
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279 <param name="kofam_subset" value="SUBSET"/>
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280 </conditional>
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281 <param name="k" value="ko"/>
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282 <section name="ap">
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283 <conditional name="f_cond">
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284 <param name="f_sel" value="mapper-one-line"/>
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285 </conditional>
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286 </section>
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287 <output name="out_result" ftype="txt">
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288 <assert_contents>
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289 <has_n_lines n="7"/>
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290 <has_line line="sp|P19858|LDHA_BOVIN"/>
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291 </assert_contents>
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292 </output>
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293 </test>
0
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294 </tests>
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295 <help><![CDATA[
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296 .. class:: infomark
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297
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298 **What it does**
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299
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300 KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model.
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301
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302 KofamScan assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam (a customized HMM database of KEGG Orthologs (KOs)). K number assignments with scores above the predefined thresholds for individual KOs are more reliable than other proposed assignments. Such high score assignments are highlighted with asterisks '*' in the output. The K number assignments facilitate the interpretation of the annotation results by linking the user's sequence data to the KEGG pathways and EC numbers.
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303
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304 **Input**
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305
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306 - a query file in FASTA format with one or more amino acid sequences. Each sequence must have a unique name. A name of a sequence is a string between the header symbol (">") and the first blank character (whitespace, tab, line break, etc.). Do not put a whitespace right after ">".
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307
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308 ::
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309
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310 >sp|P00325|ADH1B_HUMAN Alcohol dehydrogenase 1B OS=Homo sapiens GN=ADH1B PE=1 SV=2
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311 MSTAGKVIKCKAAVLWEVKKPFSIEDVEVAPPKAYEVRIKMVAVGICRTDDHVVSGNLVT
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312
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313 - a KO list file of KOfam
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314
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315 ::
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316
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317 knum threshold score_type profile_type F-measure nseq nseq_used alen mlen eff_nseq re/pos definition
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318 K00001 361.33 domain trim 0.326825 1601 1149 1538 393 13.33 0.590 alcohol dehydrogenase [EC:1.1.1.1]
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319
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320 - KOfam profile files in HMM3 format or a compressed dataset containing HMM3 profiles and HAL filtering files available `here <ftp://ftp.genome.jp/pub/db/kofam/>`_.
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321
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322 **Output**
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323
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324 - KofamScan output
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325 - HMMER results as alignments, run output and tabular summary
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326
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327 .. class:: infomark
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328
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329 **References**
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330
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331 More information are available on `GitHub <https://github.com/takaram/kofam_scan>`_ and the `KofamKOALA webserver <https://www.genome.jp/tools/kofamkoala/>`_.
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332 ]]></help>
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333 <citations>
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334 <citation type="doi">10.1093/bioinformatics/btz859</citation>
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335 </citations>
4
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336 </tool>