Mercurial > repos > sanbi-uwc > mothur_test

annotate tools/mothur/seq.error.xml @ 0:ee4fee239fe7 draft default tip

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planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool profile="16.07" id="mothur_seq_error" name="Seq.error" version="@WRAPPER_VERSION@.0">
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2 <description>assess error rates in sequencing data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 echo 'seq.error(
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10 fasta=$fasta_in,
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11 reference=$alignment.template,
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12 #if $name_in:
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13 name=$name_in,
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14 #end if
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15 #if $qual.use == "yes":
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16 qfile=$qfile_in,
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17 report=$alignreport_in,
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18 #end if
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19 #if $threshold:
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20 threshold=$threshold,
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21 #end if
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22 ignorechimeras=$ignorechimeras,
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23 #if $count:
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24 count=$count,
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25 #end if
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26 processors='\${GALAXY_SLOTS:-8}'
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27 )'
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28 | sed 's/ //g' ## mothur trips over whitespace
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29 | mothur &&
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30
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31 ## move output files to correct destination
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32 prefix="$fasta_in"
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33 && mv mothur.*.logfile "$logfile"
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34 #if 'summary' in str($output_sel).split(','):
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35 && mv \${prefix%.dat}*.error.summary "$summary_out"
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36 #end if
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37 #if 'seq' in str($output_sel).split(','):
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38 && mv \${prefix%.dat}*.error.seq "$seq_out"
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39 #end if
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40 #if 'seq_forward' in str($output_sel).split(','):
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41 && mv \${prefix%.dat}*.error.seq.forward "$seq_forward_out"
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42 #end if
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43 #if 'seq_reverse' in str($output_sel).split(','):
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44 && mv \${prefix%.dat}*.error.seq.reverse "$seq_reverse_out"
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45 #end if
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46 #if 'chimera' in str($output_sel).split(','):
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47 && mv \${prefix%.dat}*.error.chimera "$chimera_out"
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48 #end if
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49 #if 'count' in str($output_sel).split(','):
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50 && mv \${prefix%.dat}*.error.count "$count_out"
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51 #end if
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52 #if 'matrix' in str($output_sel).split(','):
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53 && mv \${prefix%.dat}*.error.matrix "$matrix_out"
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54 #end if
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55 #if 'ref_query' in str($output_sel).split(','):
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56 && mv \${prefix%.dat}*.error.ref "$ref_query_out"
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57 #end if
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58
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59 #if $qual.use == "yes":
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60 #if 'quality' in str($output_sel).split(','):
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61 && mv \${prefix%.dat}*.error.quality "$quality_out"
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62 #end if
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63 #if 'qual_forward' in str($output_sel).split(','):
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64 && mv \${prefix%.dat}*.error.qual.forward "$qual_forward_out"
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65 #end if
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66 #if 'qual_reverse' in str($output_sel).split(','):
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67 && mv \${prefix%.dat}*.error.qual.reverse "$qual_reverse_out"
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68 #end if
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69 #end if
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70 ]]></command>
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71 <inputs>
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72 <param name="fasta_in" type="data" format="mothur.align" label="fasta - Candidate Sequences" help="sequences must be aligned"/>
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73 <conditional name="alignment">
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74 <param name="source" type="select" label="Select Reference Template from" help="">
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75 <option value="ref">Cached Reference</option>
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76 <option value="history">Your History</option>
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77 </param>
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78 <when value="ref">
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79 <param name="template" type="select" label="reference - Select an alignment database" help="">
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80 <options from_data_table="mothur_aligndb"/>
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81 </param>
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82 </when>
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83 <when value="history">
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84 <param name="template" type="data" format="mothur.align" label="reference - Reference to align with" help=""/>
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85 </when>
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86 </conditional>
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87 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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88 <conditional name="qual">
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89 <param name="use" type="select" label="Include a quality file and an alignment report as inputs" help="">
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90 <option value="no">No</option>
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91 <option value="yes">Yes</option>
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92 </param>
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93 <when value="yes">
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94 <param name="qfile_in" type="data" format="qual" label="qfile - Fasta Quality"/>
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95 <param name="alignreport_in" type="data" format="mothur.align.report" label="alignreport - Align Report"/>
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96 </when>
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97 <when value="no"/>
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98 </conditional>
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99 <param name="count" type="data" format="mothur.count_table" optional="true" label="The count parameter allows you to provide a count file associated with your fasta file, so you can include the redundant sequences in your error analysis"/>
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100 <param name="threshold" type="float" value="" min="0" max="1" optional="true" label="threshold - error rate at which to report (default 1.)"/>
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101 <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/>
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102 <param name="output_sel" type="select" multiple="true" display="checkboxes" label="Outputs as history datasets">
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103 <option value="summary">error.summary</option>
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104 <option value="seq">error.seq</option>
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105 <option value="seq_forward">error.seq.forward</option>
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106 <option value="seq_reverse">error.seq.reverse</option>
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107 <option value="chimera">error.chimera</option>
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108 <option value="count">error.count</option>
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109 <option value="matrix">error.matrix</option>
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110 <option value="quality">error.quality</option>
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111 <option value="qual_forward">error.qual.forward</option>
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112 <option value="qual_reverse">error.qual.reverse</option>
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113 <option value="ref_query">error.ref-query</option>
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114 </param>
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115 </inputs>
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116 <outputs>
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117 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
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118 <data name="summary_out" format="tabular" label="${tool.name} on ${on_string}: error.summary">
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119 <filter>'summary' in output_sel</filter>
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120 </data>
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121 <data name="seq_out" format="fasta" label="${tool.name} on ${on_string}: error.seq">
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122 <filter>'seq' in output_sel</filter>
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123 </data>
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124 <data name="seq_forward_out" format="tabular" label="${tool.name} on ${on_string}: error.seq.forward">
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125 <filter>'seq_forward' in output_sel</filter>
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126 </data>
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127 <data name="seq_reverse_out" format="tabular" label="${tool.name} on ${on_string}: error.seq.reverse">
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128 <filter>'seq_reverse' in output_sel</filter>
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129 </data>
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130 <data name="chimera_out" format="tabular" label="${tool.name} on ${on_string}: error.chimera">
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131 <filter>'chimera' in output_sel</filter>
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132 </data>
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133 <data name="count_out" format="tabular" label="${tool.name} on ${on_string}: error.count">
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134 <filter>'count' in output_sel</filter>
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135 </data>
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136 <data name="matrix_out" format="tabular" label="${tool.name} on ${on_string}: error.matrix">
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137 <filter>'matrix' in output_sel</filter>
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138 </data>
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139 <data name="quality_out" format="tabular" label="${tool.name} on ${on_string}: error.quality">
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140 <filter>qual['use'] == 'yes' and 'quality' in output_sel</filter>
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141 </data>
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142 <data name="qual_forward_out" format="tabular" label="${tool.name} on ${on_string}: error.qual.forward">
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143 <filter>qual['use'] == 'yes' and 'qual_forward' in output_sel</filter>
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144 </data>
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145 <data name="qual_reverse_out" format="tabular" label="${tool.name} on ${on_string}: error.qual.reverse">
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146 <filter>qual['use'] == 'yes' and 'qual_reverse' in output_sel</filter>
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147 </data>
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148 <data name="ref_query_out" format="mothur.align" label="${tool.name} on ${on_string}: error.ref-query">
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149 <filter>'ref_query' in output_sel</filter>
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150 </data>
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151 </outputs>
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152 <tests>
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153 <test><!--test with all outputs and no qual file-->
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154 <param name="fasta_in" value="amazon.align_head" ftype="mothur.align"/>
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155 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
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156 <param name="source" value="history"/>
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157 <param name="output_sel" value="summary,seq,seq_forward,seq_reverse,chimera,count,matrix,ref_query"/>
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158 <output name="chimera_out" md5="9faf0da7d724a1db5e0d8f5fcb72b486"/>
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159 <output name="count_out" md5="9aea787346ad6a1c496aa1d77262a487"/>
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160 <output name="matrix_out" md5="b7d9bbf3cdf363b41551e31c0b460a47"/>
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161 <output name="ref_query_out" md5="42b42eb4c6bc2705ded2c697a757106f"/>
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162 <output name="seq_out" md5="5a884846a8d94b8482c2935d2e7e43e6"/>
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163 <output name="seq_forward_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
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164 <output name="seq_reverse_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
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165 <output name="summary_out" md5="04abbbd6aa82f084e4a3bd51c4ce98e6"/>
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166 <expand macro="logfile-test"/>
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167 </test>
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168 <test><!--test with qual file and all outputs -->
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169 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
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170 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
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171 <param name="source" value="history"/>
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172 <param name="output_sel" value="summary,seq,seq_forward,seq_reverse,chimera,count,matrix,ref_query,quality,qual_forward,qual_reverse"/>
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173 <param name="use" value="yes"/>
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174 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/>
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175 <param name="alignreport_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report"/>
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176 <output name="chimera_out" md5="78e586f1a1362fd98808d7725d786caa"/>
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177 <output name="count_out" md5="ee987c7b5dc90d4d3a0ef55d817cc540"/>
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178 <output name="matrix_out" md5="6b9310b4acd95c560cd062b620b35826"/>
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179 <output name="ref_query_out" md5="dd569264c5a4628079de3ef828766e90"/>
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180 <output name="quality_out" md5="844b50d6642381a7f434b8182b9307da"/>
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181 <output name="qual_forward_out" md5="371fc760fc51b5adf10044fc26c1bbb8"/>
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182 <output name="qual_reverse_out" md5="81f17617ba99cac5807e454a626eb006"/>
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183 <output name="seq_out" md5="69a8ec131df0b1d4d95eaeb04e057941"/>
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184 <output name="seq_forward_out" md5="dbcbbefdc83c2a7c045e3930850cdbd9"/>
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185 <output name="seq_reverse_out" md5="5618b1e431306ec1275f1572d6c0c2fc"/>
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186 <output name="summary_out" md5="d33bddf9b112f2f3a80b38cf7ac50e6a"/>
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187 <expand macro="logfile-test"/>
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188 </test>
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189 </tests>
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190 <help>
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191 <![CDATA[
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192
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193 @MOTHUR_OVERVIEW@
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194
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195 **Command Documenation**
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196
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197 The seq.error_ command evaluates error rate for sequences by comparing to the fasta-formatted template_alignment_.
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198 This is demonstrated in http://www.mothur.org/wiki/Schloss_SOP#Error_analysis
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199
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200 .. _template_alignment: http://www.mothur.org/wiki/Alignment_database
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201 .. _seq.error: http://www.mothur.org/wiki/Seq.error
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202
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203 ]]>
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204 </help>
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205 <expand macro="citations"/>
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206 </tool>