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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
author iuc
date Thu, 10 Aug 2023 06:53:23 +0000
parents 8979c288aefb
children
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6
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
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1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.2+galaxy@VERSION_SUFFIX@" profile="22.05">
2
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2 <description>converter from FASTX-toolkit</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 <command detect_errors="exit_code"><![CDATA[
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8 @CATS@ fastq_to_fasta
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9 $SKIPN
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10 $RENAMESEQ
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11 -v @FQQUAL@
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12 #if $compress_output == 'yes' or ($compress_output == 'infer' and ($input.ext.endswith('.gz') or $input.ext.endswith('.bz2'))):
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13 | gzip -c > '$output_gz'
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14 #else:
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15 > '$output'
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16 #end if
2
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17 ]]></command>
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18 <inputs>
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19 <expand macro="fastq_input" />
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20 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
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21 <option value="">yes</option>
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22 <option value="-n">no</option>
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23 </param>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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24 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
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25 <option value="-r">yes</option>
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26 <option value="">no</option>
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27 </param>
5
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28 <param name="compress_output" type="select" label="Compress output FASTA">
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29 <option value="infer" selected="true">Infer from input data</option>
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30 <option value="yes">Yes</option>
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31 <option value="no">No</option>
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32 </param>
2
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33 </inputs>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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34 <outputs>
5
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35 <data name="output" format="fasta" metadata_source="input" label="${tool.name} on ${on_string}: FASTA">
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36 <filter>
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37 compress_output == 'no' or compress_output == 'infer' and not (input.ext.endswith('.gz') or input.ext.endswith('.bz2'))
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38 </filter>
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39 </data>
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40 <data name="output_gz" format="fasta.gz" metadata_source="input" label="${tool.name} on ${on_string}: FASTA.gz">
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41 <filter>
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42 compress_output == 'yes' or compress_output == 'infer' and input.ext.endswith('.gz') or input.ext.endswith('.bz2')
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43 </filter>
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44 </data>
2
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45 </outputs>
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46 <tests>
5
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47 <test expect_num_outputs="1" >
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48 <!-- 1 FASTQ-To-FASTA, keep N, don't rename -->
2
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49 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
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50 <param name="SKIPN" value=""/>
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51 <param name="RENAMESEQ" value=""/>
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52 <output name="output" file="fastq_to_fasta1a.out" />
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53 </test>
5
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54 <test expect_num_outputs="1" >
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55 <!-- 2 FASTQ-To-FASTA, discard N, rename -->
2
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56 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
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57 <param name="SKIPN" value="no"/>
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58 <param name="RENAMESEQ" value="yes"/>
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59 <output name="output" file="fastq_to_fasta1b.out" />
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60 </test>
5
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61 <test expect_num_outputs="1" >
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62 <!-- 3 FASTQ-To-FASTA, discard N, rename -->
2
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63 <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" />
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64 <param name="SKIPN" value="no"/>
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65 <param name="RENAMESEQ" value="yes"/>
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66 <output name="output" file="fastq_to_fasta-out2.out" />
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67 </test>
5
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68 <test expect_num_outputs="1" >
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69 <!-- 4 Infer FASTQ.GZ-To-FASTA.GZ -->
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70 <param name="input" value="fastq_to_fasta-in2.fastq.gz" ftype="fastqsanger.gz" />
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71 <param name="SKIPN" value="no"/>
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72 <param name="RENAMESEQ" value="yes"/>
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73 <param name="compress_output" value="infer"/>
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74 <output name="output" file="fastq_to_fasta-out2.out.gz" compare="sim_size" delta="50" />
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75 </test>
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76 <test expect_num_outputs="1" >
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77 <!-- 5 Force FASTQ.GZ-To-FASTA -->
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78 <param name="input" value="fastq_to_fasta-in2.fastq.gz" ftype="fastqsanger.gz" />
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79 <param name="SKIPN" value="no"/>
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80 <param name="RENAMESEQ" value="yes"/>
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81 <param name="compress_output" value="no"/>
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82 <output name="output" file="fastq_to_fasta-out2.out"/>
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83 </test>
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84 <test expect_num_outputs="1" >
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85 <!-- 6 Force FASTQ-To-FASTA.GZ -->
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86 <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" />
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87 <param name="SKIPN" value="no"/>
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88 <param name="RENAMESEQ" value="yes"/>
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89 <param name="compress_output" value="yes"/>
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90 <output name="output" file="fastq_to_fasta-out2.out.gz" compare="sim_size" delta="50" />
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91 </test>
2
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92 </tests>
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93 <help><![CDATA[
0
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94 **What it does**
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95
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96 This tool converts data from Solexa format to FASTA format (scroll down for format description).
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97
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98 --------
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99
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100 **Example**
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101
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102 The following data in Solexa-FASTQ format::
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103
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104 @CSHL_4_FC042GAMMII_2_1_517_596
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105 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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106 +CSHL_4_FC042GAMMII_2_1_517_596
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107 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
1
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108
0
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109 Will be converted to FASTA (with 'rename sequence names' = NO)::
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110
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111 >CSHL_4_FC042GAMMII_2_1_517_596
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112 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
1
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113
0
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114 Will be converted to FASTA (with 'rename sequence names' = YES)::
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115
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116 >1
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117 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
1
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118
0
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119 ------
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120
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121 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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122
1
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123 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
2
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124 ]]></help>
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125 <expand macro="citations" />
0
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126 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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127 </tool>