Mercurial > repos > iuc > mothur_seq_error

annotate seq.error.xml @ 11:2714e215de97 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Thu, 21 Jan 2021 23:25:34 +0000
parents 98a736c61a4a
children
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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="stdio"/>
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8 <expand macro="version_command"/>
1
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## create symlinks to input datasets
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13 ln -s '$fasta_in' fasta_in.dat &&
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14 ln -s '$name_in' name_in.dat &&
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15 ln -s '$count' count.dat &&
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16 ln -s '$alignment.template' alignment.template.dat &&
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17 #if $qual.use == "yes":
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18 ln -s '$qual.qfile_in' qfile_in.dat &&
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19 ln -s '$qual.alignreport_in' alignreport_in.dat &&
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20 #end if
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21
3
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22 echo 'seq.error(
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23 fasta=fasta_in.dat,
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24 reference=alignment.template.dat,
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25 #if $name_in:
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26 name=name_in.dat,
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27 #end if
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28 #if $qual.use == "yes":
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29 qfile=qfile_in.dat,
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30 report=alignreport_in.dat,
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31 #end if
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32 #if $threshold:
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33 threshold=$threshold,
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34 #end if
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35 ignorechimeras=$ignorechimeras,
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36 #if $count:
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37 count=count.dat,
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38 #end if
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39 #if $fasta_in.is_of_type('mothur.align')
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40 aligned=T,
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41 #else
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42 aligned=F,
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43 #end if
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44 processors='\${GALAXY_SLOTS:-8}'
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45 )'
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46 | sed 's/ //g' ## mothur trips over whitespace
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47 | mothur
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48 | tee mothur.out.log
0
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49 ]]></command>
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50 <inputs>
1
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51 <param name="fasta_in" type="data" format="mothur.align,fasta" label="fasta - Candidate Sequences" help="sequences must be aligned"/>
0
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52 <conditional name="alignment">
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53 <param name="source" type="select" label="Select Reference Template from" help="">
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54 <option value="ref">Cached Reference</option>
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55 <option value="history">Your History</option>
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56 </param>
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57 <when value="ref">
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58 <param name="template" type="select" label="reference - Select an alignment database" help="">
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59 <options from_data_table="mothur_aligndb"/>
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60 </param>
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61 </when>
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62 <when value="history">
1
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63 <param name="template" type="data" format="mothur.align,fasta" label="reference - Reference to align with" help=""/>
0
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64 </when>
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65 </conditional>
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66 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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67 <conditional name="qual">
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68 <param name="use" type="select" label="Include a quality file and an alignment report as inputs" help="">
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69 <option value="no">No</option>
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70 <option value="yes">Yes</option>
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71 </param>
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72 <when value="yes">
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73 <param name="qfile_in" type="data" format="qual" label="qfile - Fasta Quality"/>
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74 <param name="alignreport_in" type="data" format="mothur.align.report" label="alignreport - Align Report"/>
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75 </when>
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76 <when value="no"/>
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77 </conditional>
1
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78 <param name="count" type="data" format="mothur.count_table" optional="true" label="count table"/>
0
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79 <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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80 <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/>
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81 <expand macro="param-savelog"/>
0
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82 </inputs>
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83 <outputs>
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84 <expand macro="logfile-output"/>
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85 <data name="summary_out" format="tabular" from_work_dir="fasta_in*.error.summary" label="${tool.name} on ${on_string}: error.summary">
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86 <filter>'summary' in output_sel</filter>
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87 </data>
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88 <data name="seq_out" format="fasta" from_work_dir="fasta_in*.error.seq" label="${tool.name} on ${on_string}: error.seq">
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89 <filter>'seq' in output_sel</filter>
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90 </data>
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91 <data name="seq_forward_out" format="tabular" from_work_dir="fasta_in*.error.seq.forward" label="${tool.name} on ${on_string}: error.seq.forward">
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92 <filter>'seq_forward' in output_sel</filter>
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93 </data>
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94 <data name="seq_reverse_out" format="tabular" from_work_dir="fasta_in*.error.seq.reverse" label="${tool.name} on ${on_string}: error.seq.reverse">
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95 <filter>'seq_reverse' in output_sel</filter>
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96 </data>
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97 <data name="chimera_out" format="tabular" from_work_dir="fasta_in*.error.chimera" label="${tool.name} on ${on_string}: error.chimera">
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98 <filter>'chimera' in output_sel</filter>
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99 </data>
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100 <data name="count_out" format="tabular" from_work_dir="fasta_in*.error.count" label="${tool.name} on ${on_string}: error.count">
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101 <filter>'count' in output_sel</filter>
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102 </data>
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103 <data name="matrix_out" format="tabular" from_work_dir="fasta_in*.error.matrix" label="${tool.name} on ${on_string}: error.matrix">
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104 <filter>'matrix' in output_sel</filter>
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105 </data>
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106 <data name="quality_out" format="tabular" from_work_dir="fasta_in*.error.quality" label="${tool.name} on ${on_string}: error.quality">
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107 <filter>qual['use'] == 'yes' and 'quality' in output_sel</filter>
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108 </data>
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109 <data name="qual_forward_out" format="tabular" from_work_dir="fasta_in*.error.qual.forward" label="${tool.name} on ${on_string}: error.qual.forward">
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110 <filter>qual['use'] == 'yes' and 'qual_forward' in output_sel</filter>
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111 </data>
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112 <data name="qual_reverse_out" format="tabular" from_work_dir="fasta_in*.error.qual.reverse" label="${tool.name} on ${on_string}: error.qual.reverse">
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113 <filter>qual['use'] == 'yes' and 'qual_reverse' in output_sel</filter>
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114 </data>
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115 <data name="ref_query_out" format="mothur.align" from_work_dir="fasta_in*.error.ref" label="${tool.name} on ${on_string}: error.ref-query">
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116 <filter>'ref_query' in output_sel</filter>
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117 </data>
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118 </outputs>
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119 <tests>
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120 <test><!--test with all outputs and no qual file-->
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121 <param name="fasta_in" value="amazon.align_head" ftype="mothur.align"/>
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122 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
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123 <param name="source" value="history"/>
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124 <param name="output_sel" value="summary,seq,seq_forward,seq_reverse,chimera,count,matrix,ref_query"/>
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125 <output name="chimera_out" md5="9faf0da7d724a1db5e0d8f5fcb72b486"/>
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126 <output name="count_out" md5="9aea787346ad6a1c496aa1d77262a487"/>
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127 <output name="matrix_out" md5="b7d9bbf3cdf363b41551e31c0b460a47"/>
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128 <output name="ref_query_out" md5="42b42eb4c6bc2705ded2c697a757106f"/>
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129 <output name="seq_out" md5="5a884846a8d94b8482c2935d2e7e43e6"/>
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130 <output name="seq_forward_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
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131 <output name="seq_reverse_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
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132 <output name="summary_out" md5="04abbbd6aa82f084e4a3bd51c4ce98e6"/>
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133 <param name="savelog" value="true"/>
0
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134 <expand macro="logfile-test"/>
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135 </test>
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136 <test><!--test with qual file and all outputs -->
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137 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
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138 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
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139 <param name="source" value="history"/>
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140 <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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141 <param name="use" value="yes"/>
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142 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/>
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143 <param name="alignreport_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report"/>
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144 <output name="chimera_out" md5="78e586f1a1362fd98808d7725d786caa"/>
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145 <output name="count_out" md5="ee987c7b5dc90d4d3a0ef55d817cc540"/>
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146 <output name="matrix_out" md5="6b9310b4acd95c560cd062b620b35826"/>
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147 <output name="ref_query_out" md5="dd569264c5a4628079de3ef828766e90"/>
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148 <output name="quality_out" md5="844b50d6642381a7f434b8182b9307da"/>
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149 <output name="qual_forward_out" md5="371fc760fc51b5adf10044fc26c1bbb8"/>
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150 <output name="qual_reverse_out" md5="81f17617ba99cac5807e454a626eb006"/>
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151 <output name="seq_out" md5="69a8ec131df0b1d4d95eaeb04e057941"/>
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152 <output name="seq_forward_out" md5="dbcbbefdc83c2a7c045e3930850cdbd9"/>
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153 <output name="seq_reverse_out" md5="5618b1e431306ec1275f1572d6c0c2fc"/>
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154 <output name="summary_out" md5="d33bddf9b112f2f3a80b38cf7ac50e6a"/>
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155 <param name="savelog" value="true"/>
0
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156 <expand macro="logfile-test"/>
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157 </test>
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158 </tests>
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159 <help><![CDATA[
0
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160
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161 @MOTHUR_OVERVIEW@
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162
1
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163 **Command Documentation**
0
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164
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165 The seq.error_ command evaluates error rate for sequences by comparing to the fasta-formatted template_alignment_.
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98a736c61a4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ff56a4c9218ddea84ff5cd72fd98c62db212465d"
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166 This is demonstrated in https://mothur.org/wiki/miseq_sop/#assessing-error-rates
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167
1
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168 .. _template_alignment: https://www.mothur.org/wiki/Alignment_database
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169 .. _seq.error: https://www.mothur.org/wiki/Seq.error
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170
3
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171 ]]></help>
7
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172 <expand macro="citations">
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173 <citation type="doi">10.1371/journal.pone.0027310</citation>
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174 </expand>
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175 </tool>