Mercurial > repos > iuc > mothur_remove_seqs

annotate remove.seqs.xml @ 10:d38f2ac5db71 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 12:22:09 +0000
parents 0b8ca0026f28
children
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0
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_remove_seqs" name="Remove.seqs" version="@WRAPPER_VERSION@.0">
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Remove sequences by name</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
10
d38f2ac5db71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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6 <expand macro="biotools"/>
0
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10 <command><![CDATA[
2
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11 @SHELL_OPTIONS@
0
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12
2
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13 ## if accnos file is empty, just output files as-is, mothur errors if accnos empty (e.g. chimera filtering in pipeline but sample had no chimeras)
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14 #import os
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15 #if $os.lstat(str($accnos)).st_size == 0:
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16 echo "accnos file empty, nothing to remove, skipping step"
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17 #if $fasta_in:
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18 && cp $fasta_in $fasta_out
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19 #end if
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20 #if $fastq_in:
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21 && cp $fastq_in $fastq_out
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22 #end if
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23 #if $count_in:
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24 && cp $count_in $count_out
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25 #end if
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26 #if $qfile_in:
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27 && cp $qfile_in $qfile_out
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28 #end if
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29 #if $name_in:
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30 && cp $name_in $name_out
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31 #end if
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32 #if $group_in:
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33 && cp $group_in $group_out
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34 #end if
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35 #if $alignreport_in:
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36 && cp $alignreport_in $alignreport_out
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37 #end if
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38 #if $list_in:
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39 && cp $list_in $list_out
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40 #end if
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41 #if $taxonomy_in:
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42 && cp $taxonomy_in $taxonomy_out
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43 #end if
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44 #else:
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45 ## create symlinks to input datasets
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46 ln -s '$accnos' accnos.dat &&
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47 ln -s '$fasta_in' fasta_in.dat &&
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48 ln -s '$fastq_in' fastq_in.dat &&
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49 ln -s '$count_in' count_in.dat &&
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50 ln -s '$qfile_in' qfile_in.dat &&
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51 ln -s '$name_in' name_in.dat &&
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52 ln -s '$group_in' group_in.dat &&
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53 ln -s '$alignreport_in' alignreport_in.dat &&
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54 ln -s '$list_in' list_in.dat &&
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55 ln -s '$taxonomy_in' taxonomy_in.dat &&
0
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56
2
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57 echo 'remove.seqs(
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58 accnos=accnos.dat
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59 #if $fasta_in:
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60 ,fasta=fasta_in.dat
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61 #end if
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62 #if $fastq_in:
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63 ,fastq=fastq_in.dat
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64 #end if
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65 #if $count_in:
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66 ,count=count_in.dat
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67 #end if
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68 #if $qfile_in:
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69 ,qfile=qfile_in.dat
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70 #end if
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71 #if $name_in:
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72 ,name=name_in.dat
0
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73 #end if
2
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74 #if $group_in:
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75 ,group=group_in.dat
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76 #end if
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77 #if $alignreport_in:
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78 ,alignreport=alignreport_in.dat
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79 #end if
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80 #if $list_in:
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81 ,list=list_in.dat
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82 #end if
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83 #if $taxonomy_in:
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84 ,taxonomy=taxonomy_in.dat
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85 #end if
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86 $dups
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87 )'
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88 | sed 's/ //g' ## mothur trips over whitespace
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89 | mothur
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90 | tee mothur.out.log
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91 #end if
0
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92 ]]></command>
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93 <inputs>
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94 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names of sequences to be removed"/>
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95 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
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96 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
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97 <param name="fastq_in" type="data" format="fastq" optional="true" label="fastq"/>
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98 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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99 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/>
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100 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
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101 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
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102 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
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103 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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104 <param name="dups" type="boolean" truevalue="" falsevalue=",dups=false" checked="true" label="dups - Apply to duplicates"/>
2
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105 <expand macro="param-savelog"/>
0
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106 </inputs>
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107 <outputs>
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108 <expand macro="logfile-output"/>
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109 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in.pick.dat" label="${tool.name} on ${on_string}: pick.fasta">
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110 <filter>fasta_in</filter>
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111 </data>
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112 <data name="fastq_out" format_source="fastq_in" from_work_dir="fastq_in.pick.dat" label="${tool.name} on ${on_string}: pick.fastq">
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113 <filter>fastq_in</filter>
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114 </data>
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115 <data name="count_out" format_source="count_in" from_work_dir="count_in.pick.dat" label="${tool.name} on ${on_string}: pick.count">
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116 <filter>count_in</filter>
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117 </data>
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118 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in.pick.dat" label="${tool.name} on ${on_string}: pick.qfile">
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119 <filter>qfile_in</filter>
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120 </data>
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121 <data name="name_out" format="mothur.names" from_work_dir="name_in.pick.dat" label="${tool.name} on ${on_string}: pick.names">
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122 <filter>name_in</filter>
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123 </data>
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124 <data name="group_out" format="mothur.groups" from_work_dir="group_in.pick.dat" label="${tool.name} on ${on_string}: pick.groups">
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125 <filter>group_in</filter>
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126 </data>
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127 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in.pick.dat" label="${tool.name} on ${on_string}: pick.align.report">
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128 <filter>alignreport_in</filter>
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129 </data>
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130 <data name="list_out" format="mothur.list" from_work_dir="list_in.pick.dat" label="${tool.name} on ${on_string}: pick.list">
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131 <filter>list_in</filter>
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132 </data>
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133 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in.pick.dat" label="${tool.name} on ${on_string}: pick.taxonomy">
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134 <filter>taxonomy_in</filter>
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135 </data>
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136 </outputs>
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137 <tests>
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138 <test>
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139 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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140 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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141 <param name="dups" value=""/>
2
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142 <param name="savelog" value="true"/>
0
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143 <expand macro="logfile-test"/>
2
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144 <output name="fasta_out">
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145 <assert_contents>
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146 <expand macro="test-fasta-format"/>
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147 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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148 </assert_contents>
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149 </output>
0
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150 </test>
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151 <test>
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152 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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153 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
2
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154 <param name="savelog" value="true"/>
0
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155 <expand macro="logfile-test"/>
2
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156 <output name="fastq_out">
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157 <assert_contents>
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158 <expand macro="test-fastq-format"/>
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159 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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160 </assert_contents>
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161 </output>
0
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162 </test>
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163 <test><!-- test two input files -->
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164 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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165 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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166 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
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167 <param name="dups" value=",dups=false"/>
2
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168 <param name="savelog" value="true"/>
0
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169 <expand macro="logfile-test"/>
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170 <output name="fasta_out">
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171 <assert_contents>
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172 <expand macro="test-fasta-format"/>
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173 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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174 </assert_contents>
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175 </output>
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176 <output name="fastq_out">
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177 <assert_contents>
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178 <expand macro="test-fastq-format"/>
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179 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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180 </assert_contents>
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181 </output>
0
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182 </test>
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183 <test>
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184 <param name="accnos" value="amazon.bad.accnos"/>
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185 <param name="count_in" value="amazon.count_table"/>
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186 <param name="savelog" value="true"/>
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187 <expand macro="logfile-test"/>
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188 <output name="count_out">
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189 <assert_contents>
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190 <expand macro="test-count-format"/>
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191 <has_text text="U68595"/>
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192 </assert_contents>
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193 </output>
0
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194 </test>
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195 <!-- TODO: make test for empty accnos file -->
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196 </tests>
2
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197 <help><![CDATA[
0
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198
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199 @MOTHUR_OVERVIEW@
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200
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201 **Command Documentation**
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202
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203 The remove.seqs_ command takes a list of sequence names and either a fasta, name_, group_, list_, align.report_ or taxonomy_ file to generate a new file that does not contain the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection.
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204
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205 .. _name: https://www.mothur.org/wiki/Name_file
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206 .. _group: https://www.mothur.org/wiki/Group_file
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207 .. _list: https://www.mothur.org/wiki/List_file
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208 .. _align.report: https://www.mothur.org/wiki/Align.seqs
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209 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
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210 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
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211 .. _remove.seqs: https://www.mothur.org/wiki/Remove.seqs
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212
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213 ]]></help>
0
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214 <expand macro="citations"/>
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215 </tool>