Mercurial > repos > rhpvorderman > fast_fastq_filter

annotate fast_fastq_filter.xml @ 1:6ee24ca51829 draft default tip

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"planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
author rhpvorderman
date Wed, 08 Jun 2022 07:49:43 +0000
parents 5f0d949db99e
children
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1
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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1 <tool id="fast_fastq_filter" name="fastq-filter" version="0.3.0" python_template_version="3.5" profile="16.04">
0
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2 <description>filter FASTQ reads fast</description>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
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3 <requirements>
1
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4 <requirement type="package" version="0.3.0">fastq-filter</requirement>
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5 <!-- TODO: Remove this once biocontainer is published -->
1
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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6 <container type="docker">quay.io/rhpvorderman/fastq-filter:0.3.0</container>
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7 </requirements>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
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8 <command detect_errors="exit_code"><![CDATA[
1
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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9 set -e;
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10 fastq-filter
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11 #if str($filters.minimum_length.enabled) == "true"
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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12 --min-length $filters.minimum_length.threshold
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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13 #end if
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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14 #if str($filters.maximum_length.enabled) == "true"
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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15 --max-length $filters.maximum_length.threshold
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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16 #end if
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17 #if str($filters.average_error_rate.enabled) == "true"
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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18 --average-error-rate $filters.average_error_rate.threshold
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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19 #end if
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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20 #if str($filters.mean_quality.enabled) == "true"
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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21 --mean-quality $filters.mean_quality.threshold
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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22 #end if
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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23 #if str($filters.median_quality.enabled) == "true"
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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24 --median-quality $filters.median_quality.threshold
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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25 #end if
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26 --verbose
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27 -o '${output1}.gz'
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28 #if str($library.type) == "paired":
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29 -o ${output2}.gz
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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30 #end if
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31
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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32 '$library.input_1'
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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33 #if str($library.type) == "paired":
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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34 '$library.input_2'
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35 #end if
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36 ;
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37
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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38 mv '${output1}.gz' '$output1';
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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39 #if str($library.type) == "paired":
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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40 mv '${output2}.gz' '$output2';
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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41 #end if
0
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42 ]]></command>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
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43 <inputs>
1
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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44 <conditional name="library">
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45 <param name="type" type="select" label="Single-end or Paired-end reads?">
6ee24ca51829 "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
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46 <option value="single">Single-end</option>
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47 <option value="paired">Paired-end</option>
0
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48 </param>
1
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49 <when value="single">
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50 <param type="data" name="input_1" label="Input FASTQ file" format="fastqsanger,fastqsanger.gz" />
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51 </when>
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52 <when value="paired">
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53 <param type="data" name="input_1" label="Input FASTQ file #1" format="fastqsanger,fastqsanger.gz" />
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54 <param type="data" name="input_2" label="Input FASTQ file #2" format="fastqsanger,fastqsanger.gz" />
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55 </when>
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56 </conditional>
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57 <section name="filters" title="Filters" expanded="true">
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58 <conditional name="minimum_length">
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59 <param name="enabled" type="boolean" label="Minimum length"
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60 help="The minimum length for a read."/>
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61 <when value="true">
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62 <param name="threshold" type="integer" label="Threshold"
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63 value="20" min="1"/>
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64 </when>
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65 <when value="false"/>
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66 </conditional>
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67 <conditional name="maximum_length">
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68 <param name="enabled" type="boolean" label="Maximum length"
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69 help="The maximum length for a read."/>
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70 <when value="true">
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71 <param name="threshold" type="integer" label="Threshold"
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72 value="1000" min="1"/>
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73 </when>
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74 <when value="false"/>
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75 </conditional>
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76 <conditional name="average_error_rate">
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77 <param name="enabled" type="boolean" label="Average error rate"
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78 help="The minimum average per base error rate."/>
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79 <when value="true">
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80 <param name="threshold" type="float" label="Threshold"
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81 value="0.001" min="0"/>
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82 </when>
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83 <when value="false"/>
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84 </conditional>
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85 <conditional name="mean_quality">
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86 <param name="enabled" type="boolean" label="Mean quality">
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87 <help>
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88 Average quality. Same as the 'Average error rate' option but
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89 specified with a phred score. I.e a mean quality of 30 is
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90 equivalent to an average error rate of 0.001'.
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91 </help>
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92 </param>
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93 <when value="true">
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94 <param name="threshold" type="integer" label="Threshold"
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95 value="30" min="0"/>
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96 </when>
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97 <when value="false"/>
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98 </conditional>
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99 <conditional name="median_quality">
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100 <param name="enabled" type="boolean" label="Median quality">
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101 <help>
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102 DEPRECATED: The minimum median phred score. This is not as
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103 informative as the average error rate. It is also slower to
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104 calculate. This filter is only included for backwards
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105 compatibility reasons.
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106 </help>
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107 </param>
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108 <when value="true">
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109 <param name="threshold" type="integer" label="Threshold"
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110 value="30" min="0"/>
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111 </when>
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112 <when value="false"/>
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113 </conditional>
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114 </section>
0
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115 </inputs>
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116 <outputs>
1
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117 <data name="output1" format="fastqsanger.gz" />
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118 <data name="output2" format="fastqsanger.gz">
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119 <filter>library['type'] == 'paired'</filter>
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120 </data>
0
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121 </outputs>
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122 <help><![CDATA[
1
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123 When paired FASTQ data is given, fastq-filter makes sure the output is in
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124 sync. The filters behave as follows for paired-end data:
0
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125
1
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126 + average error rate: The average of the combined phred scores is used.
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127 + median quality: The median of the combined phred scores is used.
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128 + Minimum length: at least one of the records of the pair must meet the minimum length.
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129 + Maximum length: None of the records in the pair must exceed the maximum length.
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130
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131 The rationale for the length filters is that R1 and R2 both sequence the same
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132 molecule and the canonical length is the longest of both.
0
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133
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134 ]]></help>
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135 <citations>
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136 <citation type="bibtex">
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137 @misc{githubfastq-filter,
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138 author = {Vorderman, Ruben Harmen Paul},
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139 year = {2021},
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140 title = {fastq-filter},
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141 publisher = {GitHub},
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142 journal = {GitHub repository},
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143 url = {https://github.com/LUMC/fastq-filter},
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144 }</citation>
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145 </citations>
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146 </tool>