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annotate readseq.xml @ 1:36e5445b7807 draft

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author dereeper
date Tue, 08 Jan 2019 10:14:18 -0500
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1 <tool id="sniplay_readseq" name="Readseq" version="2.0.0">
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description> Convert various alignment formats </description>
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5
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6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
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7 <requirements>
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8 <requirement type="binary">perl</requirement>
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9 <requirement type="package" version="2.1.30">readseq</requirement>
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10 </requirements>
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11
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12 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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13 <stdio>
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14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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15 <exit_code range="1:" level="fatal" />
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16 </stdio>
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17
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18 <!-- [REQUIRED] The command to execute -->
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19 <command>
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20 java -jar /home/galaxy/data/jars/readseq.jar $filein -f $format >> $fileout_log 2>&amp;1 &amp;&amp;
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21 #if str( $format ) == "1":
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22 mv ${filein}.ig $fileout
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23 #elif str( $format ) == "2" :
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24 mv ${filein}.gb $fileout
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25 #elif str( $format ) == "3" :
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26 mv ${filein}.nbrf $fileout
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27 #elif str( $format ) == "4" :
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28 mv ${filein}.embl $fileout
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29 #elif str( $format ) == "5" :
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30 mv ${filein}.gcg $fileout
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31 #elif str( $format ) == "6" :
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32 mv ${filein}.strider $fileout
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33 #elif str( $format ) == "8" :
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34 mv ${filein}.fasta $fileout
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35 #elif str( $format ) == "11" :
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36 mv ${filein}.phylip2 $fileout
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37 #elif str( $format ) == "12" :
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38 perl $__tool_directory__/complete_names.pl ${filein} ${filein}.phylip $fileout
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39 #elif str( $format ) == "13" :
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40 mv ${filein}.seq $fileout
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41 #elif str( $format ) == "14" :
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42 mv ${filein}.pir $fileout
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43 #elif str( $format ) == "15" :
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44 mv ${filein}.msf $fileout
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45 #elif str( $format ) == "17" :
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46 mv ${filein}.nexus $fileout
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47 #elif str( $format ) == "18" :
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48 mv ${filein}.pretty $fileout
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49 #elif str( $format ) == "19" :
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50 mv ${filein}.xml $fileout
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51 #elif str( $format ) == "22" :
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52 mv ${filein}.aln $fileout
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53 #elif str( $format ) == "25" :
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54 mv ${filein}.ace $fileout
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55 #end if
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56 </command>
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57
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58 <!-- [REQUIRED] Input files and tool parameters -->
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59 <inputs>
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60 <param name="filein" type="data" format="fasta" optional="false" label="Fasta alignment input" />
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61 <param name="fileout_label" type="text" value="phylip conversion" label="Output name" help="Output name for files" />
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62 <param name="format" type="select" label="Output format" >
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63 <option value="1">1.IG|Stanford</option>
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64 <option value="2">2.GenBank|gb</option>
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65 <option value="3">3.NBRF</option>
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66 <option value="4">4.EMBL|em</option>
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67 <option value="5">5.GCG</option>
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68 <option value="6">6.DNAStrider</option>
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69 <option value="8">8.Pearson|Fasta|fa</option>
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70 <option value="11">11.Phylip3.2</option>
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71 <option value="12" selected="true">12.Phylip|Phylip4</option>
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72 <option value="13">13.Plain|Raw</option>
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73 <option value="14">14.PIR|CODATA</option>
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74 <option value="15">15.MSF</option>
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75 <option value="17">17.PAUP|NEXUS</option>
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76 <option value="18">18.Pretty</option>
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77 <option value="19">19.XML</option>
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78 <option value="22">22.Clustal</option>
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79 <option value="25">25.ACEDB</option>
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80 </param>
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81 </inputs>
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82
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83 <!-- [REQUIRED] Output files -->
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84 <outputs>
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85 <data name="fileout_log" format="txt" label="${fileout_label}.log" />
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86 <data name="fileout" format="txt" label="${fileout_label}" >
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87 <change_format>
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88 <when input="format" value="1" format="ig" />
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89 <when input="format" value="2" format="genbank" />
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90 <when input="format" value="4" format="embl" />
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91 <when input="format" value="5" format="gcg" />
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92 <when input="format" value="6" format="strider" />
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93 <when input="format" value="8" format="fasta" />
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94 <when input="format" value="11" format="phylip" />
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95 <when input="format" value="12" format="phylip" />
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96 <when input="format" value="14" format="pir" />
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97 <when input="format" value="17" format="nexus" />
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98 <when input="format" value="18" format="prettyseq" />
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99 <when input="format" value="19" format="xml" />
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100 <when input="format" value="22" format="clustal" />
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101 <when input="format" value="25" format="acedb" />
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102 </change_format>
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103 </data>
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104 </outputs>
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105
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106 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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107 <tests>
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108 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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109 <test>
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110 <param name="filein" value="readseq-alignment.fa" />
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111 <param name="format" value="1" />
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112 <output name="fileout" file="readseq-standford" />
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113 </test>
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114 <test>
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115 <param name="filein" value="readseq-alignment.fa" />
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116 <param name="format" value="2" />
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117 <output name="fileout" file="readseq-GenBank" />
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118 </test>
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119 <test>
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120 <param name="filein" value="readseq-alignment.fa" />
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121 <param name="format" value="3" />
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122 <output name="fileout" file="readseq-NBRF" />
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123 </test>
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124 <test>
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125 <param name="filein" value="readseq-alignment.fa" />
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126 <param name="format" value="4" />
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127 <output name="fileout" file="readseq-EMBL" />
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128 </test>
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129 <test>
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130 <param name="filein" value="readseq-alignment.fa" />
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131 <param name="format" value="5" />
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132 <assert_command>
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133 <has_text text="-f 5" />
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134 <has_text text=".gcg" />
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135 </assert_command>
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136 </test>
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137 <test>
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138 <param name="filein" value="readseq-alignment.fa" />
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139 <param name="format" value="6" />
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140 <output name="fileout" file="readseq-DNAStrider" />
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141 </test>
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142 <test>
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143 <param name="filein" value="readseq-alignment.fa" />
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144 <param name="format" value="8" />
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145 <output name="fileout" file="readseq-Pearson" />
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146 </test>
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147 <test>
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148 <param name="filein" value="readseq-alignment.fa" />
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149 <param name="format" value="11" />
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150 <output name="fileout" file="readseq-phylip32" />
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151 </test>
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152 <test>
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153 <param name="filein" value="readseq-alignment.fa" />
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154 <param name="format" value="12" />
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155 <output name="fileout" file="readseq-phylip" />
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156 </test>
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157 <test>
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158 <param name="filein" value="readseq-alignment.fa" />
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159 <param name="format" value="13" />
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160 <output name="fileout" file="readseq-raw" />
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161 </test>
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162 <test>
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163 <param name="filein" value="readseq-alignment.fa" />
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164 <param name="format" value="14" />
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165 <output name="fileout" file="readseq-PIR" />
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166 </test>
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167 <test>
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168 <param name="filein" value="readseq-alignment.fa" />
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169 <param name="format" value="15" />
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170 <output name="fileout" file="readseq-MSF.txt" lines_diff="2" />
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171 </test>
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172 <test>
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173 <param name="filein" value="readseq-alignment.fa" />
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174 <param name="format" value="17" />
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175 <output name="fileout" file="readseq-NEXUS" />
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176 </test>
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177 <test>
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178 <param name="filein" value="readseq-alignment.fa" />
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179 <param name="format" value="18" />
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180 <output name="fileout" file="readseq-Pretty" />
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181 </test>
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182 <test>
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183 <param name="filein" value="readseq-alignment.fa" />
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184 <param name="format" value="19" />
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185 <output name="fileout" file="readseq-XML" />
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186 </test>
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187 <test>
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188 <param name="filein" value="readseq-alignment.fa" />
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189 <param name="format" value="22" />
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190 <output name="fileout" file="readseq-Clustal" />
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191 </test>
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192 <test>
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193 <param name="filein" value="readseq-alignment.fa" />
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194 <param name="format" value="25" />
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195 <output name="fileout" file="readseq-ACEDB" />
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196 </test>
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197
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198 </tests>
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199
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200 <!-- [OPTIONAL] Help displayed in Galaxy -->
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201 <help><![CDATA[
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202
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203 .. class:: infomark
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204
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205 **Authors** Don Gilbert software@bio.indiana.edu
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206
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207 | **Please cite** If you use this tool, please cite Don Gilbert software@bio.indiana.edu
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208
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209 .. class:: infomark
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210
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211 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)
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212
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213 .. class:: infomark
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214
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215 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
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216
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217 ---------------------------------------------------
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218
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219 =======
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220 Readseq
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221 =======
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222
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223 -----------
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224 Description
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225 -----------
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226
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227 | Compute a phylip tree from a fasta alignment.
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228
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229 ------------
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230 Dependencies
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231 ------------
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232 ReadSeq
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233 readseq_ 2.1.30, Conda version
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234
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235 .. _readseq: https://anaconda.org/bioconda/readseq
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236
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237 ----------
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238 Input file
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239 ----------
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240
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241 Fasta file
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242 The input data file contains sequence alignment(s)
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243
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244
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245 ---------
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246 Parameter
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247 ---------
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248
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249 Output name
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250 Output base name for the ouput files
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251
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252
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253 ------------
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254 Output files
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255 ------------
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256
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257 Output_name
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258 Resulting tree in phylip format
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259
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260 Output_name.log
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261 Log file
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262
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263 ---------------------------------------------------
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264
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265 ---------------
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266 Working example
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267 ---------------
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268
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269 Input file
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270 ==========
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271
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272 Fasta file
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273 -----------
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274
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275 ::
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276
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277 >IRAT112 GAGAACCGTCCTGTAAGTACTCTTGCTTTAAGTAATAAAGTAATACTAATCCATGACGCTTAAGTCGAAGAGAGAATAAGTCAATATTTAATTGGACTCATCGCTTATTATCATTATGAATCAATAAACAACTTGATGTTGTGCTCCATGTACGATATATAAAGACAGATA
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278 >KARASUKARASURANKASU GAGAACCGTCCTGTAAGTACTCTTGCTTTAAATACGAAAGTAATACTAATCCATGACGCTTAAGTCGAAGAGAGAATAAGTCAATATTTAATTGGACTCATCGCTTATGTTCATCATGAATCTATAGTTAACTTGATGTTGTGCTCCATGTACGATATAAAAAGTTAGATA
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279
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280
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281 Parameters
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282 ==========
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283
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284 Output name -> phylip conversion
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285
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286
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287 Output file
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288 ===========
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289
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290 phylip conversion
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291 -----------------
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292
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293 ::
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294
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295 168 5125
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296 IRAT112 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT
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297 KARASUKARA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT
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298
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299 ]]></help>
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300 <citations>
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301 <citation type="doi" >10.1002/0471250953.bia01es00</citation>
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302 </citations>
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303
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304 </tool>